Methods for identifying anti-cancer compounds

ABSTRACT

Methods are provided for identifying agents capable of modulating cap-dependent RNA translation by comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system that comprises eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs. The modulation of translation in the presence of the agent indicates the agent as capable of modulating cap-dependent mRNA translation. The method can be used to identify anti-cancer agents and oncogenes that may be responsible for tumorigenesis.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to International application PCT/US2014/68875, filed Dec. 5, 2014, which in turn claims priority to U.S. Patent Application Ser. No. 61/912,420, filed Dec. 5, 2013, both of which are incorporated herein by reference in their entireties.

GOVERNMENT SUPPORT

This research was supported by funding from the National Cancer Institute Grants R01-CA142798-01 and U01CA105492-08, and National Institutes of Health Grant GM-073855. The U.S. Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

The initiation of cap-dependent translation involves ˜13 tightly controlled protein factors (reviewed in (Jackson et al., 2010)). Among these, eIF4E binds the mRNA cap structure and interacts with a scaffold (eIF4G) and the eIF4A RNA helicase (a DEAD box protein also known as DDX2). During initiation these and other factors form the eIF4F complex and together with the 40S ribosomal unit proceed to a transcript's 5′UTR for a translation start site. The eIF4A RNA helicase is directly involved in scanning and recent studies have defined co-factors and the molecular mechanics of its helicase activity (Marintchev, 2009, 2013; Parsyan et al., 2011; Svitkin, 2001). However, the precise mRNA features that necessitate the eIF4A helicase action are not known.

The activation of protein translation contributes to malignant transformation. For example, activation of the RAS, ERK, and AKT signaling pathways stimulates cap-dependent translation (reviewed in (Blagden and Willis, 2011; D'Ambrogio et al., 2013; Guertin and Sabatini, 2007). Moreover, the rate limiting eIF4E translation factor is expressed at high levels in many cancers and can transform rodent fibroblasts and promote tumor development in vivo (Lazaris-Karatzas et al., 1990; Ruggero et al., 2004; Wendel et al., 2004). Accordingly, cap-dependent translation is an emerging target for cancer therapies (see recent review by (Blagden and Willis, 2011). Notably, three distinct natural compounds target the eIF4A helicase and these are silvestrol isolated from plants in the Malaysian rainforest (Cencic, 2009), pateamine A found in marine sponges off the coast of New Zealand (Northcote et al., 1991), and hippuristanol which is produced by pacific corals (Li et al., 2009b). These compounds show promising preclinical activity against different cancers (Bordeleau et al., 2005; Bordeleau et al., 2006; Cencic et al., 2007; Schatz et al., 2011; Tsumuraya et al., 2011a). Other strategies to inhibit translation include rapamycin and mTORC1 kinase inhibitors (Hsieh et al., 2012; Thoreen et al., 2009), inhibitors of the eIF4E kinase MNK1/2 (Furic et al., 2010; Ueda et al., 2004; Wendel et al., 2007), a peptide (4EGI-1) that interferes with the eIF4E-eIF4G interaction (Moerke et al., 2007), and the anti-viral ribavirin that may bind eIF4E directly (Kentsis et al., 2004; Yan et al., 2005).

The recently developed transcriptome-scale ribosome footprinting technology greatly facilitates the study of protein translation. Briefly, the technology is based on the identification of ribosome-protected RNA fragments in relation to total transcript levels using deep sequencing (Ingolia et al., 2009). The technology has been applied to explore translational effects in various biological contexts, and perhaps the most relevant to this study are reports of the translational effects of mTORC1 inhibition on mRNAs harboring TOP- and TOP-like sequences (Hsieh et al., 2012; Thoreen et al., 2012).

BRIEF DESCRIPTION OF THE INVENTION

In one embodiment, a method is provided for identifying an agent capable of modulating cap-dependent mRNA translation. The method comprises comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs. eIF4A refers to eIF4A1 or eIF4A2, and RNA helicases include, but are not limited to, eIF4A1, eIF4A2, DHX9 or DHX36. The modulation of translation in the presence of the agent indicates the agent as capable of modulating cap-dependent mRNA translation. In one embodiment, modulating is decreasing, suppressing or inhibiting cap-dependent mRNA translation. In one embodiment, the agent stabilizes the binding of eIF4A to the eIF4A-dependent translation-controlling motif of the mRNA. In one embodiment, the eIF4A-mRNA complex stabilizing motif of the mRNA is located in the 5′ UTR.

In one embodiment, the eIF4A-dependent translation-controlling motif comprises a G-quadruplex structure. In one embodiment, the G-quadruplex structure comprises a (GGC/A)₄ motif. In one embodiment, the (GGC/A)₄ motif comprises GGCGGCGGCGGC (SEQ ID NO:1). In one embodiment, the eIF4A-dependent translation-controlling motif comprises a sequence selected from SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 or SEQ ID NO:10. In one embodiment, the eIF4A-dependent translation-controlling motif comprises a sequence selected from among SEQ ID NO:10 to SEQ ID NO:62. In one embodiment, the eIF4A-dependent translation-controlling motif is at least one sequence selected from SEQ ID NO:1 or from among SEQ ID NO:4 to SEQ ID NO:62.

In one embodiment of the methods described herein, the mRNA encodes a transcription factor. In one embodiment, the mRNA encodes an oncogene. In other embodiments, the mRNA encodes NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2. In other embodiments, the mRNA is from a gene selected from Table 3A. In other embodiments, the mRNA is from a gene selected from Table 3B. In other embodiments, the mRNA is from a gene selected from Table 3C.

In one embodiment of the method, the agent suppresses the growth of cancer cells in vitro or in vivo. In one embodiment, the agent interferes with eIF4A activity. In one embodiment, the agent increases eIF4A activity. In one embodiment, the agent inhibits eIF4A helicase activity. In one embodiment, the agent increases eIF4A helicase activity. In one embodiment, the agent promotes the stabilizing the binding of eIF4A with an eIF4A-dependent translation-controlling motif. In one embodiment, the agent does not trigger feedback activation of Akt.

In one embodiment, the modulation of translation in the foregoing method is measured by a fluorescence reporter assay. In one embodiment, the assay comprises renilla luciferase expression.

In one embodiment, a method is provided for identifying an agent that modulates eIF4A activity, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein the increase or decrease in translation efficiency in the presence of the agent indicates the agent as capable of increasing or decreasing eIF4A activity.

In one embodiment, a method is provided for identifying an agent that inhibits eIF4A activity, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the agent as capable of inhibiting eIF4A activity.

In one embodiment, a method is provided for determining whether an mRNA sequence comprises at least one eIF4A-dependent translation-controlling motif, the method comprising comparing translation efficiency in the presence and absence of an agent that inhibits eIF4A activity in an in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the mRNA sequence possesses at least one eIF4A-dependent translation-controlling motif.

In one embodiment, a method is provided for determining whether a cancer or tumor is susceptible to an agent that inhibits eIF4A activity, the method comprising identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor, wherein the presence of the at least one eIF4A-dependent translation-controlling motif indicates susceptibility of the cancer or tumor to the agent. In one embodiment, the level of expression of MYC is not predictive of the susceptibility of a cancer or tumor to an agent that inhibits eIF4A activity.

In one embodiment, methods are provided for 1) measuring the effect of known RNA helicases such as eIF4A, DHX9 or DHX36 on G-quadruplex unwinding; 2) investigating the effect of other cofactors/inhibitors required for eIF4A activity; 3) a screening method to identify other proteins that can unwind G-quadruplexes; or 4) identifying and establishing the effect of small molecules that stabilize the G-quadruplex structure, by utilizing a fluorescence resonance energy transfer (FRET)-based assay utilizing an oligonucleotide comprising a G-quadruplex labeled with a fluorophore at the 5′ or 3′ end of the oligonucleotide, and a fluorescence quencher at the other end. The aforementioned uses are merely non-limiting examples.

In one embodiment, a method for preventing, treating or intervening in the recurrence of a cancer in a subject is provided. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer. In one embodiment, the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA. In one embodiment, the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the oncogenic mRNA comprises a G-quadruplex motif. In one embodiment, the oncogenic mRNA is from an oncogene, which by way of non-limiting example is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In the foregoing embodiments, the cancer is, by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In one embodiment the subject has cancer. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma.

In one embodiment, a method is provided for preventing, treating or intervening in the recurrence of a cancer in a subject having an eIF4A dependent cancer. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer. In one embodiment, the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA. In one embodiment, the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the oncogenic mRNA comprises a G-quadruplex motif. In one embodiment, the oncogenic mRNA is from an oncogene. In one embodiment, the oncogene is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In the foregoing embodiments, the cancer is, by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In one embodiment the subject has cancer. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma.

In another embodiment, a method is provided for inhibiting in a subject the translation of an oncogene that comprises an eIF4A-dependent translation-controlling motif. The method comprises administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting translation of the oncogene. In one embodiment, translation of the oncogene causes cancer in the subject. In another embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In this embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the mRNA of the oncogene comprises a G-quadruplex motif. In one embodiment, the oncogene is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In the foregoing embodiments, the cancer is, by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In one embodiment the subject has cancer. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma.

In one embodiment, a method for inhibiting in a subject eIF4A dependent mRNA translation is provided. The method comprises administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting mRNA translation. In one embodiment, the mRNA translation causes cancer in the subject. In one embodiment, the mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the mRNA encodes an oncogenic protein. In one embodiment, the oncogenic protein is encoded by an oncogene selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In the foregoing embodiments, the cancer is, by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In one embodiment the subject has cancer. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma.

In one embodiment, a method for preventing in a subject the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby inhibiting translation of the mRNA. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the mRNA is from an oncogene selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2. In one embodiment, the translation of the mRNA causes cancer.

In the foregoing embodiments, the cancer is, by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In one embodiment the subject has cancer. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma.

In any of the foregoing embodiments, the agent blocks the activity of eIF4A helicase. In any of the foregoing embodiments, the agent blocks the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif. In any of the foregoing embodiments, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In any of the foregoing embodiments, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.

Non-limiting examples of aforementioned agents include a rocaglamide, such as silvestrol, CR-31-B, or an analogue or derivative thereof. In other embodiments, the agent is hippuristanol, pateamine A, or an analogue or derivative thereof.

U.S. Patent Application Ser. No. 61/912,420, filed Dec. 5, 2013, is incorporated herein by reference in its entirety.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows that translational activation contributes to T-ALL pathogenesis and maintenance;

FIG. 2 shows that silvestrol blocks cap-dependent translation and has single-agent activity against T-ALL;

FIG. 3 shows that transcriptome-scale ribosome footprinting can be used to define silvestrol's effects on translation;

FIG. 4 shows that silvestrol alters the distribution of ribosomes across many mRNAs;

FIG. 5 shows that many cancer genes are differentially affected by silvestrol;

FIG. 6 shows the validation of selected silvestrol targets;

FIG. 7 is a diagram depicting an eIF4A dependent mechanism of translational control;

FIG. 8 shows the PI3K pathway and translational activation in T-ALL;

FIG. 9 shows testing silvestrol and the synthetic analogue CR-31-B in T-ALL;

FIG. 10 shows ribosome profiling quality control data and effects on translation;

FIG. 11 shows analysis of genes with differential ribosomal distribution;

FIG. 12 shows gene ontology analysis of silvestrol sensitive genes;

FIG. 13 illustrates exploring the relative contribution of MYC and other silvestrol targets in T-ALL;

FIG. 14 illustrates a FRET-based assay for measuring the effect of RNA helicases on G-G-quadruplex unwinding, screening proteins that can unwind G-quadruplexes and identify small molecules that stabilize the G-quadruplex structure;

FIG. 15 shows the sensitivity of several small cell lung cancer lines to silvestrol;

FIG. 16 shows the sensitivity of several renal cell carcinoma cell lines to silvestrol;

FIG. 17 shows the sensitivity to silvestrol of a number of cancer cell lines;

FIG. 18 shows that the sensitivity of cancer cell lines to silvestrol is not predicted by MYC expression;

FIG. 19 shows activity of hippuristanol and panteamine A in the reporter assay;

FIG. 20 shows in vitro data on silvestrol on a number of lung cancer cell lines and key target proteins;

FIG. 21 shows the effect of silvestrol on lung cancer cells in the presence and absence of serum, with and without MG-132, and the effect on key target proteins;

FIG. 22 shows transcripts of KRAS, and the presence of G-quadruplex structures;

FIG. 23 compares the G-quadruplex structures in NRAS and KRAS;

FIG. 24 shows the effect of silvestrol on KRAS protein levels in PANC1 cells and the effect of various compounds on PANC1 and MiaPaca2 cells;

FIG. 25 shows the in vivo activity of silvestrol on MiaPaca2 xenografts;

FIG. 26 shows the effect in individual animals xenografted with H82 small cell lung cancer cells and treated with silvestrol, etoposide or both; and

FIG. 27 shows a summary of in vivo data for two dose levels of silvestrol and the effects on key target proteins.

DETAILED DESCRIPTION OF THE INVENTION

A mechanism of translational control has been identified that is characterized by a requirement for eIF4A/DDX2 RNA helicase activity and underlies the anticancer effects of silvestrol and related compounds. eIF4A refers to eIF4A1 or eIF4A2, and RNA helicases include, but are not limited to, eIF4A1, eIF4A2, DHX9 or DHX36. In one embodiment, activation of cap-dependent translation contributes to T-cell leukemia (T-ALL) development and maintenance. Accordingly, inhibition of the translation initiation factor eIF4A with silvestrol produces powerful therapeutic effects. By using transcriptome-scale ribosome footprinting on silvestrol-treated T-ALL cells to identify silvestrol-sensitive transcripts, the features of eIF4A-dependent translation embodied herein were identified. These features include, in one embodiment, a long 5′UTR and a 12-mer sequence motif that encodes a guanine quartet (GGC)₄. RNA folding algorithms pinpoint the (GGC)₄ motif as a common site of RNA G-quadruplex structures within the 5′UTR. In T-ALL these structures mark highly silvestrol-sensitive transcripts that include key oncogenes and transcription factors and contribute to the drug's anti-leukemic action. Hence, the eIF4A-dependent translation of G-quadruplex containing transcripts is shown as a gene-selective and therapeutically targetable mechanism of translational control.

Thus, in one embodiment, a method for identifying an agent capable of modulating cap-dependent mRNA translation is provided, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein the modulation of translation in the presence of the agent indicates the agent as capable of modulating cap-dependent mRNA translation. In some embodiments, modulating is decreasing, suppressing or inhibiting cap-dependent mRNA translation.

eIF4A-dependent translation-controlling motifs are typically present in the 5′ UTR of the mRNA. In certain embodiments, the eIF4A-dependent translation-controlling motif comprises a G-quadruplex structure. In some embodiments, the G-quadruplex structure is a (GGC/A)₄ motif (i.e., four occurrences of (G, G, C or A), each occurrence independently selected from either GGC or GGA). In some embodiments, the (GGC/A)₄ motif is GGCGGCGGCGGC (SEQ ID NO:1). In some embodiments, the eIF4A-dependent translation-controlling motif comprises GGGAC (SEQ ID NO:2) motif or GGGCC (SEQ ID NO:3). In other embodiments the eIF4A-dependent translation-controlling motif comprises SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 or SEQ ID NO:10. In other embodiments, the eIF4A-dependent translation-controlling motif comprises a sequence selected from among SEQ ID NO:10 to SEQ ID NO:62. In other embodiments, the eIF4A-dependent translation-controlling motif is at least one sequence selected from SEQ ID NO:1 or from SEQ ID NO:4 to SEQ ID NO:62.

The mRNA may have one or more eIF4A-dependent translation-controlling motifs. In one embodiment, the eIF4A-dependent translation-controlling motif is at least one (GGC/A)₄ motif. In another embodiment, the eIF4A-dependent translation-controlling motif is at least one GGGAC (SEQ ID NO:2) motif. In another embodiment, the eIF4A-dependent translation-controlling motif is at least one GGGCC (SEQ ID NO:3) motif. In another embodiment, the eIF4A-dependent translation-controlling motif is at least one 12-mer motif. In other embodiments, the mRNA may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, or more eIF4A-dependent translation-controlling motifs. In another embodiment, each eIF4A-dependent translation-controlling motif is independently selected from among SEQ ID NO:1 through and including SEQ ID NO:62.

In one embodiment, an agent identified by the methods of the invention may interfere with eIF4A activity. In one embodiment, the agent may increase eIF4A activity. In one embodiment, the agent may inhibit eIF4A helicase activity. In another embodiment, the agent may increase eIF4A helicase activity. In another embodiment, the agent can promote the stabilizing the binding of eIF4A with an eIF4A-dependent translation-controlling motif.

In another embodiment, the agent does not trigger feedback activation of Akt.

In another embodiment, the mRNA encodes a transcription factor. In another embodiment, the mRNA encodes an oncogene. In another embodiment, the mRNA encodes NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2. In another embodiment the mRNA is from a gene selected from Table 3A. In another embodiment, the mRNA is from a gene selected from Table 3B. In another embodiment, the mRNA is from a gene selected from Table 3C.

The agent identified by the methods herein may be used to treat cancer. In one embodiment, the cancer is a result of the overexpression an oncogene or transcription factor. The oncogene or transcription factor may be selected from those described herein, such as but not limited to NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2, or any described in Table 3A, 3B or 3C.

Cancer includes cancerous and precancerous conditions, including, for example, premalignant and malignant hyperproliferative diseases such as cancers of the breast, ovary, germ cell, skin, prostate, colon, bladder, cervix, uterus, stomach, lung, esophagus, blood and lymphatic system, larynx, oral cavity, as well as metaplasias, dysplasias, neoplasias, leukoplakias and papillomas of the mucous membranes, and in the treatment of Kaposi's sarcoma. These are also referred to herein as dysproliferative diseases or dysproliferation. Non-limiting examples of other cancers, tumors, malignancies, neoplasms, and other dysproliferative diseases that can be treated according to the invention include leukemias, such as myeloid and lymphocytic leukemias, lymphomas, myeloproliferative diseases, and solid tumors, such as but not limited to sarcomas and carcinomas such as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, and retinoblastoma.

In one embodiment, the compounds and uses embodied herein are directed to small cell lung cancer. In one embodiment, the compounds and uses embodied herein are directed to renal cancers. In one embodiment, the compounds and uses embodied herein are directed to neuroblastoma. In one embodiment, the compounds and uses embodied herein are directed to pancreatic cancers.

In one embodiment the agent suppresses the growth of cancer cells in vitro or in vivo.

The method of carrying out the translation assay using an in-vitro or in-vivo assay described herein may be accomplished by any of a number of methods know in the art. In one embodiment, the modulation of translation is measured by a fluorescence reporter assay. In one embodiment, the fluorescence reporter assay comprises renilla luciferase expression.

As mentioned above, certain mRNAs have longer 5′ UTRs and the eIF4A-dependent translation-controlling motif is present in the 5′ UTR. In one embodiment, the eIF4A-dependent translation-controlling motif comprises a 12-mer and the mRNA is from a gene selected from Table 3A. In another embodiment, the eIF4A-dependent translation-controlling motif comprises a 9-mer and the mRNA is from a gene selected from Table 3B. In another embodiment, eIF4A-dependent translation-controlling motif comprises a (GGC)₄ motif and the mRNA is from a gene selected from Table 3C.

In another embodiment, a method for identifying an agent that modulates eIF4A activity is provided. The method comprises comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs. An increase or decrease in translation efficiency in the presence of the agent indicates the agent as capable of increasing or decreasing eIF4A activity, respectively. The in-vitro or in-vivo translation system may be one from among those described here. The mRNA may be among those described herein. The eIF4A-dependent translation-controlling motifs may be among those described herein.

In another embodiment, a method is provided for identifying an agent that inhibits eIF4A activity, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the agent as capable of inhibiting eIF4A activity. The in-vitro or in-vivo translation system may be one from among those described here. The mRNA may be among those described herein. The eIF4A-dependent translation-controlling motifs may be among those described herein.

In another embodiment, a method is described for determining whether an mRNA sequence comprises at least one eIF4A-dependent translation-controlling motif. In this method, translation efficiency is compared in the presence and absence of an agent that inhibits eIF4A activity in an in-vitro translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the mRNA sequence possesses at least one eIF4A-dependent translation-controlling motif. By way of non-limiting example, the agent is selected from among silvestrol(methyl(1R,2R,3S,3aR,8bS)-6-[[(2S,3R,6R)-6-R1R)-1,2-dihydroxyethyl]-3-methoxy-1,4-dioxan-2-yl]oxy]-1,8b-dihydroxy-8-methoxy-3a-(4-methoxyphenyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxylate), pateamine A ((3S,6Z,8E,11S,15R,17S)-15-amino-3-[(1E,3E,5E)-7-(dimethylamino)-2,5-dimethylhepta-1,3,5-trienyl]-9,11,17-trimethyl-4,12-dioxa-20-thia-21-azabicyclo[16.2.1]henicosa-1(21),6,8,18-tetraene-5,13-dione), hippuristanol, (±)-CR-31-B, among other rocaglamide((1R,2R,3S,3aR,8bS)-1,8b-dihydroxy-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide) derivatives.

Methods are also provided for determining whether a cancer or tumor is susceptible to an agent that inhibits eIF4A activity. In one embodiment, the method comprising identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor, wherein the presence of the at least one eIF4A-dependent translation-controlling motif indicates susceptibility of the cancer or tumor to the agent. In other embodiments, the eIF4A-dependent translation-controlling motifs are among those described herein above. In one embodiment, the presence of MYC is not predictive of the susceptibility of a cancer or tumor to an agent that inhibits eIF4A activity.

In another embodiment, a method for determining whether a patient having cancer or a tumor will respond to treatment with an eIF4A inhibitor is provided comprising the steps of 1) obtaining a sample of the cancer or tumor from the patient; and 2) identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor, wherein the presence of the at least one eIF4A-dependent translation-controlling motif indicates that the patient will respond to the treatment. In the foregoing embodiments, identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor can be performed by comparing translation efficiency in the presence and absence of an eIF4A inhibitor agent in an in-vitro or in-vivo translation system comprising eIF4A and mRNA from the cancer or tumor, wherein a decrease in translation efficiency in the presence of the agent indicates the presence of an eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor. In another embodiment, identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor can be performed by identifying a G-quadruplex motif in at least one oncogene in the cancer or tumor. In certain embodiments, the motif is selected from among those described in SEQ ID NO:1 and in any one of SEQ ID NO:4-62. In certain embodiments, the expression of MYC is not correlated with responsiveness or sensitivity of a patient's cancer or tumor to an agent that inhibits eIF4A activity.

In another embodiment, a method is provided for determining whether a patient having cancer or a tumor will respond to treatment with an eIF4A inhibitor comprising the steps of 1) obtaining a sample of the cancer or tumor from the patient; and 2) identifying the presence of at least one oncogene in the cancer or tumor described in Table 3A, 3B or 3C herein, wherein the presence of said at least one oncogene indicates that the patient will respond to the treatment. In one embodiment, the presence or expression of MYC is not correlated with responsiveness or sensitivity to the treatment.

Furthermore, in other embodiments, methods to determine the level of expression of eIF4E, eIF4A, eIF4G, or eIF4B, and presence of the eIF4F complex indicate sensitivity to silvestrol and other eIF4A inhibitors, and such methods carried out in any format will be useful or determining if a tumor or patient's cancer will be sensitive to silvestrol. In another embodiment, measuring the expression of Mdr1/p-glycoprotein, a resistance marker for silvestrol, indicates the eIF4A inhibitors may be less effective and require a different dosing regimen, such as but not limited to dose level and dosing frequency. In another embodiment, expression of other helicases, e.g. DHX9 and DHX36, may causes resistance to silvestrol and thus useful in identifying cancers or tumors that may not be sensitive to silvestrol, to guide the chemotherapeutic regimen to the optimal benefit of the patient.

In one embodiment, methods are provided for 1) measuring the effect of known RNA helicases such as eIF4A, DHX9 or DHX36 on G-quadruplex unwinding; 2) investigating the effect of other cofactors/inhibitors required for eIF4A activity; 3) a screening method to identify other proteins that can unwind G-quadruplexes; and 4) identifying and establishing the effect of small molecules that stabilize the G-quadruplex structure. These methods among others may be achieved by use of a fluorescence resonance energy transfer (FRET)-based assay utilizing an oligonucleotide comprising a G-quadruplex labeled with a fluorophore at the 5′ or 3′ end of the oligonucleotide, and a fluorescence quencher at the other. In one non-limiting example, a FRET-labeled GC-quadruplex is 5′-UAGAA ACUAC GGCGG CGGCG GAAUC GUAGA (SEQ ID NO:65) and a mutant oligonucleotide without the G-quadruplex is UAGACCCUGCAACGUCAGCGUAGUCGUAGC (SEQ ID NO:66). The 5′-end is labeled with fluorophore FAM and quencher BHQ1 on the 3′end. When folded, the labeled G-quadruplex RNA oligonucleotide will exhibit minimum baseline fluorescence. Addition of specific RNA helicase such as EIF4A with ATP and/or small molecules results in unwinding and increase in fluorescence signal measured in real time. The aforementioned FRET-labeled G-quadruplex containing oligonucleotide is merely one example and those comprising other G-quadruplexes such as but not limited to SEQ ID NOS:1-64, and in particular SEQ ID NOS:1-62 may be employed for this purpose, with other fluorophores and quencher pairs well known in the art.

This assay can therefore be used for the aforementioned purpose as well as various other purposes such as but not limited to 1) measuring the effect of known RNA helicases such as eIF4A, DHX9 or DHX36 on G-quadruplex unwinding; 2) investigating the effect of other cofactors/inhibitors required for eIF4A activity; 3) a screening method to identify other proteins that can unwind G-quadruplexes; and 4) identifying and establishing the effect of small molecules that stabilize the G-quadruplex structure.

In addition to the various embodiments described above, methods are also provided for treating a subject having cancer, and for preventing cancer in a subject at risk or recurrence in a patient in remission. Based on the findings herein that translation of oncogenes comprising an eIF4A-dependent translation-controlling motifs is dependent on eIF4A helicase activity, blocking eIF4A helicase activity is a means to prevent oncogenic protein production and prevent oncogenesis. As described herein, numerous cancer-related genes including oncogenes and transcription factors are dependent on eIF4A for translation. Heretofore, the role of eIF4A was unclear but the present studies show, inter alia, that specific motifs on oncogenic mRNAs depend on eIF4A for translation, thus blocking eIF4A helicase is a heretofore unappreciated anti-cancer mechanism. Use of agents that target eIF4A dependent translation can thus stop translation of oncogenic mRNA sequences.

In further embodiments, methods are provided for reducing or preventing recurrence of cancer in a patient in remission or otherwise considered cured. In these embodiments, the cancer is any among those described herein among others, and by way of non-limiting examples, T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma and pancreatic cancer. In other embodiments, the cancer is transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, Ewing sarcoma and lung adenocarcinoma. In one embodiment the subject has cancer. Other cancers are described in FIG. 17 are included herein, as well as the cell lines representative of such cancers. In one embodiment, the subject is at risk for developing cancer. In one embodiment, the subject is in remission from cancer.

Among these methods, administering to the subject an agent that blocks eIF4a helicase activity prevents, treats or intervenes in the recurrence of the cancer. In one embodiment, a method for preventing, treating or intervening in the recurrence of a cancer in a subject is provided. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer. In one embodiment, the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA. In one embodiment, the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the oncogenic mRNA comprises a G-quadruplex motif. In one embodiment, the oncogenic mRNA is from an oncogene, which by way of non-limiting example is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In one embodiment, a method is provided for preventing, treating or intervening in the recurrence of a cancer in a subject having an eIF4A dependent cancer. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer. In one embodiment, the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA. In one embodiment, the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the oncogenic mRNA comprises a G-quadruplex motif. In one embodiment, the oncogenic mRNA is from an oncogene. In one embodiment, the oncogene is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In another embodiment, a method is provided for inhibiting in a subject the translation of an oncogene that comprises an eIF4A-dependent translation-controlling motif. The method comprises administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting translation of the oncogene. In one embodiment, translation of the oncogene causes cancer in the subject. In another embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In this embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the mRNA of the oncogene comprises a G-quadruplex motif. In one embodiment, the oncogene is selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In one embodiment, a method for inhibiting in a subject eIF4A dependent mRNA translation is provided. The method comprises administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting mRNA translation. In one embodiment, the mRNA translation causes cancer in the subject. In one embodiment, the mRNA comprises an eIF4A-dependent translation-controlling motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the mRNA encodes an oncogenic protein. In one embodiment, the oncogenic protein is encoded by an oncogene selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.

In one embodiment, a method for preventing in a subject the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif. The method comprises administering to the subject an agent that blocks eIF4a helicase activity, thereby inhibiting translation of the mRNA. In one embodiment, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In one embodiment, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62. In one embodiment, the mRNA is from an oncogene selected from among Tables 3A, 3B and 3C. In one embodiment, the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2. In one embodiment, the translation of the mRNA causes cancer.

In any of these embodiments, the agent blocks the activity of eIF4A helicase. In any of the foregoing embodiments, the agent blocks the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif. In any of the foregoing embodiments, the eIF4A-dependent translation-controlling motif is a G-quadruplex motif. In any of the foregoing embodiments, the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.

Non-limiting examples of aforementioned agents include a rocaglamide, such as silvestrol, CR-31-B, or any active analogue or derivative thereof. In other embodiments, the agent is hippuristanol, pateamine A, or any active analogue or derivative thereof. Other examples of suitable agents include those described in WO2011/140334 (based on PCT/US2011/035351).

Hallmark features are described here of eIF4A-dependent translation and defines specific 5′UTR elements that confer a requirement for that RNA helicase. The key features are longer 5′UTRs, a 12-mer (GGC)₄ motif, and related 9-mer variant motifs. Importantly, the 12-mer and 9-mer motifs precisely localize to between 53% and 65% of all predicted RNA G-quadruplex structures (depending on the analysis tool). The 9-mer sequences require neighboring nucleotides to complete the structure as the minimal number is 12 nucleotides, and it was frequently observed that more than 12 nucleotides contribute to the G-quadruplex. Moreover, most of the remaining G-quadruplexes are based on highly similar sequence elements. On the other hand IRES mRNAs are somewhat protected, while TOP, TOP-like, or PRTE elements do not appear to influence the eIF4A requirement. This is distinct from mTORC1 inhibition, which affects a different set of transcripts marked by TOP and TOP-like elements (Thoreen et al., 2012). These findings identify sequence motifs that represent translational control elements encoded in the 5′UTR of several hundred transcripts and that confer a requirement for eIF4A RNA helicase action.

RNA G-quadruplex structures are typically made from at least two stacks of four guanosines exhibiting non-Watson-Crick interactions (e.g. hydrogen bonds) and connected by one or more linker nucleotides (reviewed in (Bugaut and Balasubramanian, 2012)). In the examples herein, the linker is most often a cytosine and less frequently an adenosine. There is variation in the exact structural composition and sequence requirement as our examples illustrate. The minimum requirement for the structure is a (GGC/A)₄ sequence and neighboring nucleotides can complete the structure.

The cap-binding protein eIF4E is limiting for cap-dependent translation and its signaling control by mTORC1 and 4E-BP has been studied in great detail (Jackson et al., 2010). The results described here indicate that for a set of mRNAs the eIF4A helicase activity is required and represents the point of attack for three natural compounds, silvestrol, hippuristanol, and pateamine (Cencic et al., 2007). Moving forward, an intriguing question concerns the physiological control of eIF4A activity (Parsyan et al., 2011). In this regard, recent studies have defined the mechanics of eIF4A action (Marintchev, 2013; Marintchev et al., 2009), identified mutually exclusive potentially regulatory interactions between eIF4A and the eIF4B, eIF4G, and eIF4H factors (Rozovsky et al., 2008), and further implicated S6 kinase in the phosphorylation and signaling control of eIF4B (Kroczynska, 2009; Shahbazian et al., 2010; Shahbazian et al., 2006). The data herein indicate that these interactions define a broadly relevant layer of translational control that is distinct from the control of eIF4E by 4E-BP and mTORC1, and that is specifically aimed at a subset of transcripts.

In one embodiment, the novel sequence motifs and/or G-quadruplex structures are present in a large number of transcription factors, several known oncogenes, but also some tumor suppressor genes. A number of examples are listed and suggest that an eIF4A dependent program of translational control may have broad ramification on a cell's biology. Several genetic lesions implicated in translational activation can promote T-ALL development (e.g. PTEN, IL7R) (Palomero et al., 2007; Zenatti et al., 2011; Zhang et al., 2012).

Examples Materials and Methods

Ribosome Footprinting. KOPTK1 cells were treated with silvestrol or DMSO for 45 minutes, followed by cycloheximide treatment for 10 minutes and then harvested for total RNA and ribosome footprint fragment isolation. Total RNA was isolated using RNA isolation kit from Qiagen (74104) and subjected to RNA sequencing. Ribosome protected fragments were isolated following published protocol (Ingolia et al., 2009). Briefly cell lysates were subjected to ribosome footprinting by nuclease treatment. Footprint fragments were purified by one step sucrose cushion and gel extraction. Deep sequencing libraries were generated from these fragments. Both total RNA and footprint fragment libraries were analyzed by sequencing on the HiSeq 2000 platform.

Sequence Alignment. Sequences were aligned to the transcripts available from the human genome sequence hg19 from UCSC public database. Ribosome footprint (RF) reads were aligned to reference genome hg19 using PALMapper (Jean et al., 2010). Only the uniquely aligned reads were used for analysis. Read length of 25- to 35-bp was selected and used to analyze the translation effect of silvestrol. Total mRNA sequencing reads were aligned to the hg19 reference using STAR (Dobin et al., 2013). The splice alignment was used, and only used the uniquely aligned reads with maximum 3 mismatches.

Footprint Profile Analysis. The genome annotation was from GENCODE project (http://www.gencodegenes.org/releases/14.html). Ribosome footprint intensity (reads per million, RPM) and the expression value (reads per kilobase per million, RPKM) were measured from total mRNA-seq data and translation values were measured from ribosome footprint data. To evaluate the translation efficiency (TE) change between silvestrol- and vehicle-treated samples, TE was calculated as RPKMfootprint/RPKMmRNA (as Thoreen et al. did recently (Thoreen et al., 2012)). Changes in ribosome footprint profiles were determined by using DEXSeq algorithm (Anders et al., 2012). DEXSeq accounts for the discrete nature of the read counts and models biological variability to avoid false positives. Ratio of TEsilvestrol/TEcontrol of all the genes was plotted and color-highlighted according to the statistical significance of DEXSeq test.

Ribosome distribution analysis. The ribosomal distribution change was evaluated between silvestrol treated samples and controls. A BED file containing all non-overlapped exonic regions was generated based on genome annotation. Then the BED file and footprint BAM files were given as an input to SAMTOOLS (Li et al., 2009a) to generate new BAM files that only included exonic alignment. The exonic BAM files were input for two conditions to rDiff (Drewe et al., 2013) to identify genes that presented significant change in ribosomal distribution.

Additional Experimental Procedures

(Non-radioactive) Metabolic labeling of nascent protein. KOPTK1 cells were labeled for nascent protein synthesis using Click-iTR AHA (L-azidohomoalanine) metabolic labeling reagent obtained from Invitrogen (cat no. C10102) as per manufacturer's instructions. Briefly, following silvestrol, Cycloheximide or DMSO treated cells were incubated in methionine free medium for 30 min prior to AHA labeling for 1 hr. Cells were fixed with 4% paraformaldehyde in PBS for 15 min, permeablized with 0.25% Triton X-100 in PBS for 15 min followed by one wash with 3% BSA. Cells were then stained using Alexa Fluor 488 Alkyne (Invitrogen cat no. A10267) with Click-iT Cell reaction Buffer Kit (Invitrogen cat no. C10269). Changes in mean fluorescence intensity as a measure of newly synthesized protein was detected by Flow cytometry analysis.

Polysome profiling. KOPTK1 cells were treated with silvestrol or DMSO for 45 minutes, followed by cycloheximide treatment for 10 minutes. Cell pellet was lysed in polysome lysis buffer (300 mM NaCl, 15 mM Tris-HCl (pH 7.5), 15 mM MgCl2, 1% TritonX-100, 0.1 mg/ml Cycloheximide, 1 mg/ml Heparin). Polysome fractions were isolated using 4 ml 10-50% sucrose density gradients (300 mM NaCl, 100 mM MgCl2, 15 mM Tris-HCl (pH 7.5), 1 mg/ml Cycloheximide, 10 mg/ml Heparin). Gradients were centrifuged in an SW40Ti rotor at 35,000 rpm for 2 hrs. Fractions of 100 ul were collected manually from the top, and optical density (OD) at 254 nM was measured.

Sequence Alignment. The human genome sequence hg19 was downloaded from UCSC public database: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes. Ribosome footprint (RF) reads were aligned to reference genome hg19 using PALMapper (Jean et al., 2010). PALMapper clips the linker sequence (5′-CTGTAGGCACCATCAAT-3′), which is technically introduced during RF library construction, and trims the remaining sequence from the 3′ end while aligning the reads to reference sequence. Briefly, the parameters for PALMapper were set as follows: maximum number of mismatches: 2; maximum number of gaps: 0; minimum aligning length: 15; maximum intron length (splice alignment): 10000; minimum length of a splicing read aligned to either side of the intron boundary: 10. Only the uniquely aligned reads were used for further analysis.

To remove ribosome RNA contamination, the footprint reads were also aligned to a ribosome sequence database using PALMapper with the same parameters except allowing splice alignment. The human ribosome sequences were retrieved from BioMart Ensembl (Flicek et al., 2013) and SILVA (Quast et al., 2013) databases and merged the results into a single FASTA file, which was used as reference sequence to align against. The rRNA-aligned reads were filtered out from hg19-aligned reads.

After removing the rRNA contamination, a portion of reads were observed that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, a search was undertaken for a string of 1˜8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. The read was removed if there was no such linker sequence. Finally, reads ≦24-bp and ≧36-bp were filtered out, and the remaining reads with aligned length from 25- to 35-bp were used to analyze the translational effects of silvestrol.

Total mRNA sequencing reads were aligned to the hg19 reference using STAR (Dobin et al., 2013). The splice alignment was performed and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.

Footprint Profile Analysis. For each gene, only the number of aligned reads were counted that were mapped within exonic regions. The genome annotation was downloaded from GENCODE project (http://www.gencodegenes.org/releases/14.html). Ribosome footprint intensity (reads per million, RPM) was calculated as RPM=Ci/(N/106), where Ci is the read count for gene i, and N is the library size of silvestrol- or vehicle-treated samples. In order to eliminate the effluence of rRNA contamination, the library size was calculated after read filtering described previously. Similarly, the expression value measured from total mRNA-seq data and translation value measured from ribosome footprint data (both were referred as reads per kilobase per million, RPKM) were calculated as RPKM=Ci/(Ki·N/106), where Ki is the non-overlapped exonic region of each gene. To evaluate the translation efficiency (TE) change between silvestrol- and vehicle-treated samples, TE=RPKMfootprint/RPKMmRNA was calculated as Thoreen et al did recently (Thoreen et al., 2012).

To detect the genes that ribosome footprint profiles were significantly changed between silvestrol treated sample and control, DEXSeq (Anders et al., 2012) was used to perform the statistical test. DEXSeq accounts for the discrete nature of the read counts and it also models the biological variability which has been demonstrated in other applications to be crucial to avoid a great number of false positives. Here, DEXSeq was used in a specific way: the footprint and mRNA-seq read counts were fit into DEXseq framework, in which silvestrol treatment and control are two biological conditions, and then tested whether footprint (consisting 2 replicates for each condition) and mRNA-seq (The 3 replicates were split and recombined into two combinations such that each of them consists of two replicates) read counts were significantly different in the two conditions. The log-ratio of normalized read counts of silvestrol treated sample to control indicated whether ribosome footprint profile was increased or decreased. In the end, the ratio of TEsilvestrol/TEcontrol of all the genes was plotted, and color-highlighted them according to the statistical significance of the DEXSeq test.

In addition to studying the translation efficiency, the ribosomal distribution change was also evaluated between silvestrol treated sample and control. First, a BED file contained all non-overlapped exonic regions was generated based on genome annotation. Then the BED file and footprint BAM files were given as an input to SAMTOOLS (Li et al., 2009) to generate new BAM files only included exonic alignment. The exonic BAM files of two conditions to rDiff (Drewe et al., 2013) were input to identify genes that presented significant change in ribosomal distribution. In detail, a nonparametric test was performed implemented in rDiff to detect differential read densities. rDiff takes relevant read information, such as the mapping location and the read structure, to measure the significance of changes in the read density within a given gene between two conditions. The minimal read length was set to 25-bp, and number of permutation was set to 10000.

To plot the ribosomal distribution curves for multiple genes, read coverage of each transcript was normalized by the mean coverage value of that particular transcript. Then the UTR and coding exon length were normalized in proportion to the overall average length of corresponding regions of a group of genes. Finally all the normalized transcripts were averaged together in a vectorized way to plot the coverage distribution. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.

Motif analysis. The transcripts of each gene were quantified based on the total mRNA-seq data using MISO (Katz et al., 2010). The 5′UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME (Bailey, 2011). Over- and under-represented motifs were determined with three different settings: searching for motifs of length greater than or equal to six, nine and twelve base pairs. The predicted consensus sequences with P<1×10-4 were considered as significant motifs. The secondary structure of different gene sets was predicted using RNAfold (Hofacker, 2003) based on the same 5′UTR prepared before.

5′UTR sequences for respective group of targets were subjected to motif prediction using online available program RegRNA (A Regulatory RNA motifs and Elements Finder) (http://regrna.mbc.nctu.edu.tw/html/prediction.html) and looked specifically for motifs that occur in 5′UTR. Statistical significance for the results obtained was calculated using Fisher's exact test for count data.

T-ALL samples. Thirty-six bone marrow biopsies were collected from patients with T-ALL at multiple organizations (Universitair Ziekenhuis (UZ) Ghent, Ghent, Belgium; UZ Leuven, Leuven, Belgium; Hôpital Purpan, Toulouse, France; Centre Hospitalier Universitaire (CHU) de Nancy-Brabois, Vandoeuvre-Les-Nancy, France). The QIAamp DNA Mini kit was used to obtain genomic DNA (Qiagen 51304). The Medical Ethical Commission of Ghent University Hospital (Ghent, Belgium, B67020084745) approved this study.

Mutation analysis. NOTCH1 (exons 26, 27, 28 and 34), FBXW7 (exons 7, 8, 9, 10 and 11), PTEN (exons 1 till 9) and IL7R (exon 6) were amplified and sequenced using primers as reported in (Mavrakis et al., 2011; Shochat et al., 2011; Zuurbier et al., 2012). FBXW7, PTEN and IL7R amplification were performed using 20 ng of genomic DNA, 1×KapaTaq reaction buffer (KapaBiosystems), 1U KapaTaq DNA polymerase, 0.2 mM dNTP, 2.5 μM MgCl2, 0.2 mM forward and reverse primer in a 25 μl PCR reaction. For NOTCH1 amplification, the PCRx enhancer system (Invitrogen) was used for the PCR reaction. Reactions contained 20 ng of DNA, 2.5 U KapaTaq DNA Polymerase, 1×PCRx Amplification Buffer, 2×PCRx Enhancer Solution, 0.2 mM dNTP, 1.5 mM MgSO4 and 0.2 mM of each primer. The PCR steps were: 95° C. for 10 minutes, (96° C. for 15 sec, 57° C. for 1 minute, then 72° C. for 1 min) for 40 cycles, then 72° C. for 10 minutes. Purified PCR products were analyzed using the Applied Biosystems 3730XL DNA Analyze.

Array Complete Genomic Hybridization. PTEN deletions and MYC amplifications were detected by array CGH analysis using SurePrint G3 Human 4×180K CGH Microarrays (Agilent Technologies). First, random prime labeling of the T-ALL DNA sample and a control human reference DNA was performed with Cy3 and Cy5 dyes (Perkin Elmer), respectively. The subsequent hybridization protocol was performed according to the manufacturer's instructions (Agilent Technologies). The data was analyzed using arrayCGHbase (Menten et al., 2005).

Immunohistochemistry and Tissue Microarrays. T-cell acute lymphoblastic leukemia tissue microarrays were made as previously published (Schatz et al., 2011) using an automated tissue arrayer (Beecher Instruments, ATA-27). T-ALL samples were ascertained at Memorial Sloan-Kettering Cancer Center and were approved with an Institutional Review Board Waiver and approval of the Human Biospecimen Utilization Committee. All cancer biopsies were evaluated at MSKCC, and the histological diagnoses were based on haematoxylin and eosin (H&E) staining. TMAs were stained with the c-MYC polyclonal antibody (Epitomics 51242) using Discovery XT (Ventana) for 1 hour and a secondary anti-rabbit antibody (Vector Laboratories) for 1 hour. Histological images were captured using a Zeiss Axiocam MRc through a Zeiss Achropla lens on an Axioskop 40 microscope. Images were processed for brightness and contrast using Axiovision Rel. 4.6. Cores were scored as 0, 1, or 2 reflecting the fraction of positive cells.

Generation of mice. The ICN-driven mouse T-ALL model has been reported (Pear et al., 1996; Wendel et al., 2004). Data were analyzed in Kaplan-Meier format using the log-rank (Mantel-Cox) test for statistical significance. The surface marker analysis was as described (Wendel et al., 2004). ShRNAs against Pten and Fbxw7 have been reported in (Mavrakis et al., 2011).

Tumor transplantation. Leukemic bone marrow from mice expressing the ICN and IK6 was infected with OMOMYC and selected using puromycin. 2,000,000 cells were injected into syngeneic recipients via tail vein. Mice were monitored by blood analysis. Upon leukemia detection, tamoxifen (50 mg/kg) or vehicle treatment was performed on alternating days until mice were moribund. Severe leukemia reflects >100,000 blasts/μl and led to rapid demise of animals if untreated, whereas complete remission was defined as the absence of GFP positive leukemic blasts in the blood and bone marrow.

Real-Time Quantitative PCR. Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (Qiagen 80004). Normal CD3+ T-cell RNA mixed from healthy donors was purchased from Miltenyi Biotec (130-093-164). cDNA was made using SuperScript III First-Strand (Invitrogen 18080-400). Analysis was performed by ΔΔCt. Applied Biosystems Taqman GeneExpression Assays: human Myc Hs00153408_m1, hsa-miR-19b RT and TM 396, Rnu6b RT and TM 001093, and mouse Myc Mm00487804_m1.

T-ALL cell lines. T-ALL cell lines were cultured in RPMI-1640 (Invitrogen, CA), 20% fetal calf serum, 1% penicillin/streptomycin, and 1% L-glutamine. The MOHITO line was supplemented with 5 ng/mL IL2 (Fitzgerald 30R-A1022 and 10 ng/mL of IL7 (Fitzgerald 30R-AI084X).

Immunoblots. Lysates were made using Laemli lysis buffer. 30 ug of protein was loaded onto SDS-PAGE gels then transferred onto Immobilon-FL Transfer Membranes (Millipore IPFL00010). The antibodies used were α-Tubulin (Sigma T5168), β-actin (Sigma A5316), Myc (Santa Cruz Biotechnology sc-40), p-Akt 308 (Cell Signaling 9275), Akt (Cell Signaling 9272), S6 (Cell Signaling 2317), and p-S6 (Cell Signaling 2215), Notch1 (Cell signaling 3608), Myb (Santa Cruz Biotechnology, sc-517), CDK6 (Cell Signaling 3136), EZH2 (Cell Signaling 5246), Mdm2 (Santa Cruz Biotechnology, sc-965), Bcl2 (Santa Cruz Biotechnology, sc-509), Run×1 (Cell Signaling 4336), and GAPDH (Cell Signaling 5174).

Luciferase assays. Four tandem repeats of the (CGG)4 12-mer motif (GQs) or random sequence matched for length and GC content (random) were cloned into the 5′UTR of Renilla luciferase plasmid pGL4.73. Empty firefly luciferase plasmid pGL4.13 or HCV-IRES firefly were used as internal controls. Luciferase assays were performed using Dual-Luciferase Reporter Assay System (Promega E1960) following the manufacturer's instructions. GQs sequence:

(SEQ ID NO: 63) CTAGGTTGAAAGTACTTTGACGGCGGCGGCGGTCAATCTTACGGCGGCGG CGGACATAGATACGGCGGCGGCGGTAGAAACTACGGCGGCGGCGGATTA GAATAGTAAA

Random Sequence:

(SEQ ID NO: 64) CTAGGGCGCACGTACTTCGACAACGTCAGCGTTCAGCGTTCCAACGTCAG CGTACAGCGATCCAACGTCAGCGTTCTGCGCTACAACGTCAGCGTATCCG CGTAGCACA

Statistical analysis. All Kaplan-Meier curves were analyzed using the Mantel-Cox test. The significance of xenografted tumor size differences was determined using two-way repeated measures ANOVA tests. RT-PCRs were analyzed with two tailed t-tests.

Xenografts. 5,000,000 KOPT-K1 cells in 30% matrigel (BD 354234) were injected subcutaneously into C.B-17 scid mice. When tumors were readily visible, the mice were injected on 7 consecutive days with either 0.5 mg/kg silvestrol, 0.2 mg/kg (±)-CR-31-B, or every other day with 1 mg tamoxifen. Tumor size was measured daily by caliper. P-values were calculated using 2-way repeated measures ANOVA.

Silvestrol and (±)-CR-31-B. Each was suspended in DMSO for in vitro experiments and 5.2% Tween 80 5.2% PEG 400 for in vivo experiments. Cycloheximide (C7698) and Rapamycin (R8781) were purchased from Sigma.

Toxicity studies. Eight week-old C57Bl/6NTac female mice were randomly assigned to either control or treatment groups. Each treatment group received one daily dose of test article through i.p. injection over 5 consecutive days. Toxicity was monitored by weight loss and daily clinical observation for the 14 days following test article administration. 24 hours after the last test article administration 4 mice in each group were sacrificed and clinical chemistry, hematology and tissue specific histopathology were done at autopsy. The remaining mice (n=2 per group) were kept under observation for an additional 13 days; at that point all mice were sacrificed and clinical chemistry, hematology and tissue specific histopathology were done at time of autopsy.

References for Materials and Methods:

-   Anders, S., Reyes, A., and Huber, W. (2012). Detecting differential     usage of exons from RNA-seq data. Genome research 22, 2008-2017. -   Bailey, T. L. (2011). DREME: motif discovery in transcription factor     ChIP-seq data. Bioinformatics 27, 1653-1659. -   Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C.,     Jha, S., Batut, P., Chaisson, M., and Gingeras, T. R. (2013). STAR:     ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21. -   Drewe, P., Stegle, O., Hartmann, L., Kahles, A., Bohnert, R.,     Wachter, A., Borgwardt, K., and Ratsch, G. (2013). Accurate     detection of differential RNA processing. Nucleic acids research 41,     5189-5198. -   Flicek, P., Ahmed, I., Amode, M. R., Barrell, D., Beal, K., Brent,     S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., et al.     (2013). Ensembl 2013. Nucleic acids research 41, D48-55. -   Hofacker, I. L. (2003). Vienna RNA secondary structure server.     Nucleic acids research 31, 3429-3431. -   Jean, G., Kahles, A., Sreedharan, V. T., De Bona, F., and Ratsch, G.     (2010). RNA-Seq read alignments with PALMapper. Current protocols in     bioinformatics/editoral board, Andreas D Baxevanis [et al] Chapter     11, Unit 11 16. -   Katz, Y., Wang, E. T., Airoldi, E. M., and Burge, C. B. (2010).     Analysis and design of RNA sequencing experiments for identifying     isoform regulation. Nature methods 7, 1009-1015. -   Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer,     N., Marth, G., Abecasis, G., Durbin, R., and Genome Project Data     Processing, S. (2009). The Sequence Alignment/Map format and     SAMtools. Bioinformatics 25, 2078-2079. -   Mavrakis, K. J., Van Der Meulen, J., Wolfe, A. L., Liu, X., Mets,     E., Taghon, T., Khan, A. A., Setty, M., Rondou, P., Vandenberghe,     P., et al. (2011). A cooperative microRNA-tumor suppressor gene     network in acute T-cell lymphoblastic leukemia (T-ALL). Nat Genet     43, 673-678. -   Menten, B., Pattyn, F., De Preter, K., Robbrecht, P., Michels, E.,     Buysse, K., Mortier, G., De Paepe, A., van Vooren, S., Vermeesch,     J., et al. (2005). arrayCGHbase: an analysis platform for     comparative genomic hybridization microarrays. BMC bioinformatics 6,     124. -   Pear, W. S., Aster, J. C., Scott, M. L., Hasserjian, R. P., Soffer,     B., Sklar, J., and Baltimore, D. (1996). Exclusive development of T     cell neoplasms in mice transplanted with bone marrow expressing     activated Notch alleles. The Journal of experimental medicine 183,     2283-2291. -   Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza,     P., Peplies, J., and Glockner, F. O. (2013). The SILVA ribosomal RNA     gene database project: improved data processing and web-based tools.     Nucleic acids research 41, D590-596. -   Schatz, J. H., Oricchio, E., Wolfe, A. L., Jiang, M., Linkov, I.,     Maragulia, J., Shi, W., Zhang, Z., Rajasekhar, V. K., Pagano, N. C.,     et al. (2011). Targeting cap-dependent translation blocks converging     survival signals by AKT and PIM kinases in lymphoma. The Journal of     experimental medicine 208, 1799-1807. -   Shochat, C., Tal, N., Bandapalli, O. R., Palmi, C., Ganmore, I., to     Kronnie, G., Cario, G., Cazzaniga, G., Kulozik, A. E., Stanulla, M.,     et al. (2011). Gain-of-function mutations in interleukin-7     receptor-alpha (IL7R) in childhood acute lymphoblastic leukemias.     The Journal of experimental medicine 208, 901-908. -   Thoreen, C. C., Chantranupong, L., Keys, H. R., Wang, T., Gray, N.     S., and Sabatini, D. M. (2012). A unifying model for mTORC1-mediated     regulation of mRNA translation. Nature 485, 109-113. -   Wendel, H. G., De Stanchina, E., Fridman, J. S., Malina, A., Ray,     S., Kogan, S., Cordon-Cardo, C., Pelletier, J., and Lowe, S. W.     (2004). Survival signalling by Akt and eIF4E in oncogenesis and     cancer therapy. Nature 428, 332-337. -   Zuurbier, L., Petricoin, E. F., Vuerhard, M. J., Calvert, V., Kooi,     C., Buijs-Gladdines, J., Smits, W. K., Sonneveld, E., Veerman, A.     J., Kamps, W. A., et al. (2012). The significance of PTEN and AKT     aberrations in pediatric T-cell acute lymphoblastic leukemia.     Haematologica. 2012 September; 97(9):1405-13.

Example 1 Cap-Dependent Translation in Oncogenesis

NOTCH-driven T-ALL exemplifies the frequent activation of AKT/mTORC1 and cap-dependent translation seen in cancer. For example, in a small series of pediatric T-ALLs the common NOTCH1 HD and PEST domain mutations were confirmed (56%; 20/36 samples) (O'Neil et al., 2007; Weng et al., 2006), PTEN mutations (14%; 5/36), and PTEN deletions (11%; 4/36), resulting in mono- (16%) or bi-allelic (6%) PTEN loss (Gutierrez et al., 2009; Palomero et al., 2007; Zhang et al., 2012), and occasional IL7R mutation (3%) (Zenatti et al., 2011) (FIG. 8 A-C, Table 1).

These mutations contribute to T-cell leukemogenesis. Briefly, murine hematopoietic precursor cells (HPCs) expressing Notchl intracellular fragment (ICN) alone or in combination with additional alleles were transplanted and disease latency measured in recipient animals (FIG. 1A) (Mavrakis et al., 2011; Pear et al., 1996). Notch-ICN caused T-ALL in three months (n=14, mean latency 91.5 days), while co-expression of a short-hairpin RNA (shRNA) against Pten cut average latency in half (n=10, p<0.0001; mean latency 47.1 days) (FIG. 1B, FIG. 8D). Similarly, expression of the mutant IL7r allele (IL7R/p.L242-L243insNPC (Zenatti et al., 2011), n=4, p<0.0001, mean latency 35.5 days), or the Akt oncogene (n=4, p<0.0001, mean latency 33.5 days) dramatically accelerated leukemia onset. Notably, expression of the cap-binding protein eIF4E was sufficient to reduce latency to one month (n=4, p<0.0001, mean latency 30.75 days). Pathologically all leukemias were composed of CD4/CD8 double positive cells, and immunohistochemistry showed abundant Ki67 expression and increased S6 phosphorylation in the PTEN deficient, IL7R and AKT expressing T-ALLs (FIG. 8 E/F). Hence, the cap-binding protein eIF4E is sufficient to promote NOTCH-induced T-ALL.

A genetic approach was then used to test the requirement for eIF4E in maintaining the leukemic cells. Briefly, the 4E-binding protein (4E-BP) sequesters eIF4E and blocks cap-dependent translation (Rousseau et al., 1996). 4E-BP is negatively regulated by sequential phosphorylation at several serine residues by mTORC1, and mutation of these sites results in a constitutively active 4E-BP1 (4E-BP1(4A)) allele (Rong et al., 2008). In mixed populations of murine T-ALL cells where a fraction of cells express either 4E-BP1(4A) and GFP or an empty vector and compete with un-transduced parental cells, rapid elimination was seen of 4E-BP1(4A)/GFP expressing cells from the culture (FIG. 1D/E). Hence, eIF4E activity is required to maintain T-ALL, which indicates that targeting translation might be a therapeutic strategy.

FIG. 1 depicts the translational activation in T-ALL pathogenesis and maintenance. A) Diagram of the NOTCH-ICN-driven murine T-ALL model. B) Kaplan-Meier analysis showing time to leukemia development after transplantation of HPC transduced with NOTCH1-ICN and empty vector (black, n=9), eIF4E (green, n=4), IL7r p.L242-L243insNPC (P1) (blue, n=4), shPten (orange, n=10), or Akt (red, n=4). C) Experimental design of competition experiments and potential outcomes. D) Results as percentage of each starting GFP positive population of murine T-ALL cells partially transduced with vector/GFP or the constitutive inhibitory 4E-binding protein (4E-BP1 (4A)).

FIG. 8 depicts the PI3K pathway and translational activation in T-ALL. A-C) Diagram of mutations in human T-ALL affecting PTEN (A), IL7R (B), and NOTCH1 (C). D) Immunoblots of lysates from ICN-driven murine leukemia with the additional indicated construct, probed as indicated. E) Representative FACS profiles measuring levels of the indicated markers in murine leukemia; F) Surface marker expression on murine leukemic cells of indicated genotype (+ and − indicate < or ≧50% positive cells). G) Representative histology detailing the pathological appearance of murine T-ALLs harboring the indicated genes and stained as indicated.

Example 2 Silvestrol Blocks Cap-Dependent Translation and is Active Against T-Cell Leukemia

Based on this genetic evidence a pharmacological inhibitor was then tested. Silvestrol is perhaps the best-characterized inhibitor of the eIF4F complex, it does not target eIF4E and instead blocks the eIF4A RNA helicase by stabilizing its mRNA bound form (Bordeleau et al., 2008; Cencic, 2009). Silvestrol, and a synthetic rocaglamide analogue (±)-CR-31-B (CR) bind the same site on eIF4A (Rodrigo et al., 2012; Sadlish et al., 2013). In a dual-luciferase reporter assay, where renilla and firefly luciferase are either capped or under control of an internal ribosomal entry site (IRES) element, both drugs were confirmed to preferentially block cap-dependent over IRES-dependent translation (Bordeleau et al., 2006) (FIG. 2A, FIG. 9A).

Silvestrol has excellent single-agent activity against T-ALL in vitro and in vivo. Silvestrol was tested against primary human T-ALL samples in vitro and observed efficient apoptosis induction with IC50 values ranging from 3 to 13 nM; and confirmed activity in established cell lines (FIG. 2B, FIG. 9B). The results were similar for similar the analogue CR (not shown). Notably, silvestrol showed equal activity against PTEN wild type and PTEN mutant cell lines and primary T-ALL cells. The least sensitive line (MOLT-16) carries a c-MYC translocation (Shima-Rich et al., 1997). Similarly, murine T-ALL cells engineered to express Akt, mutant IL7R, eIF4E, or an shRNA against Pten showed no significant difference in sensitivity indicating that silvestrol can overcome their activity (Figure S2C). In vivo both silvestrol and CR were effective against xenografted T-ALL cells (FIG. 2C, Figure S2D/E). Treatment of KOPT-K1 tumor (˜1 cm3) bearing NOD/SCID mice with systemic administration of silvestrol (0.5 mg/kg, d 0-6) and CR (0.2 mg/kg, d 0-6) produced a significant delay in tumor growth (Silvestrol: n=7, p<0.001; CR: n=8, p<0.001) (FIG. 2C, FIG. 9D/E). Pathologic analysis of treated tumors showed diffuse apoptosis by TUNEL and loss of proliferation by Ki-67 (FIG. 2D). Notably, no severe toxicity, death, or weight loss was observed. CR treatment at therapeutic doses showed a reversible drop in white cell count with a nadir on day 19, and no other changes in blood counts or bone marrow cytology, or serum chemistry (FIG. 9F-O, Table 2). No changes were observed in intestinal histology, which is a major concern with gamma secretase-inhibitors (FIG. 9J) (Real et al., 2009). Hence, single agent silvestrol or CR treatment is effective against T-ALL and is safe in vivo.

Silvestrol acts in a manner that is distinct from mTORC1 inhibitors. For example, the predominant inhibition of S6 kinase instead of 4E-BP and feedback activation of AKT (S308 phosphorylation) are thought to hinder the therapeutic effect of rapamycin (FIG. 2E) (Choo et al., 2008; Kang et al., 2013; Thoreen et al., 2009); 2)(O'Reilly et al., 2006; Sun et al., 2005; Thoreen et al., 2009; Wan et al., 2007). This feedback mechanism is active in KOPT-K1 cells, where Rapamycin-induced loss of ribosomal S6 phosphorylation and feedback activation of AKT (T308) was observed (FIG. 2F). By contrast, selective inhibition of eIF4A with silvestrol or CR does not affect S6 kinase activity and did not lead to phosphorylation of AKT (T308). Hence, selective inhibition of eIF4A is sufficient for therapeutic activity and avoids feedback activation of upstream AKT signaling.

FIG. 2 shows silvestrol blocks cap-dependent translation and has single-agent activity against T-ALL. A) Diagram of the dual reporter system expressing a capped renilla luciferase transcript (red) and firefly luciferase under control of the hepatitis C IRES-element (black); (below) Relative levels of renilla luciferase (red, cap-dependent) and firefly luciferase (black, IRES dependent) upon treatment with vehicle (DMSO), silvestrol or the synthetic analogue (±)-CR-31-B. B) Viability of T-ALL primary patient samples treated with silvestrol for 48 hours; PTEN status is indicated. C) Tumor size of KOPT-K1 xenografts upon treatment with (±)-CR-31-B (0.2 mg/kg) or vehicle (see Figure S2 for longer follow up and silvestrol treatment data). D) Immunohistochemistry of (±)-CR-31-B treated KOPT-K1 tumors stained as indicated. E) Simplified diagram of rapamycin and silvestrol mechanism of action. F) Lysates of KOPT-K1 cells treated with vehicle (Veh), Rapamycin (Rapa: 25 nM), (±)-CR-31-B (CR: 25 nM), or silvestrol (Silv: 25 nM) for 48 hours and probed as indicated.

FIG. 9 shows testing silvestrol and the synthetic analogue (±)-CR-31-B in T-ALL. A) Dual luciferase reporter assay, shown are relative levels of each firefly (cap-dependent) and renilla (IRES-dependent) luciferase upon treatment with silvestrol or (±)-CR-31-B. B) IC50 values for silvestrol and CR in a panel of human T-ALL lines. C) Silvestrol effect on murine T-ALLs with the indicated genetic lesions; curves are mean of triplicates and differences between the genotypes did not reach significance. D) KOPT-K1 xenograft studies. Shown is the tumor volume during and after systemic treatment with CR or vehicle (intraperitoneal injection, 0.2 mg/kg on days indicated by red arrows). E) Tumor volume upon intraperitoneal treatment with vehicle or silvestrol (0.5 mg/kg on days indicated by red arrows). F-0) Toxicity studies with (±)-CR-31-B. F) Animal weights during and after CR treatment (intraperitoneal injection, 0.2 mg/kg on days indicated by red arrows), red=CR, black=vehicle. G-I) Counts of white blood cells (G), red cells (H), and platelets (I) 14 days after cessation of CR treatment, blue lines indicate the species and strain specific reference range, n.s. indicates not significant. J) Representative histology of gastrointestinal tract (small intestine) on the indicated days during and after (±)-CR-31-B treatment; K-O) Serum levels of alanine aminotransferase (ALT) (K), aspartate transaminase (AST) (L), albumin (M), total bilirubin (N), and creatinine (O) two weeks after cessation of treatment with 0.2 mg/kg CR or vehicle, blue lines indicate the species and strain specific reference range, n.s. indicates not significant.

Example 3 Transcriptome-Scale Ribosome Footprinting Defines Silvestrol-Sensitive Translation

Next, use of the recently developed ribosome footprinting technology (Ingolia et al., 2009) was employed to measure precisely how silvestrol affected protein translation. Briefly, KOPT-K1 cells were treated with 25 nM of silvestrol or vehicle, cells collected after 45 minutes, then isolated and deep-sequenced total RNA and ribosome footprints (RFs) prepared (FIG. 3A). The early time point was chosen to capture effects on translation and minimize secondary transcriptional changes and cell death. First, RFs per mRNA were determined which, after correcting for transcript levels and length, indicated changes in translational efficiency (TE). Out of six measurements two outliers were removed (see methods); the remaining two biological replicates showed excellent consistency of read counts for each gene (Control: R2=0.90; Silvestrol: R2=0.88; data not shown). Raw reads were aligned to the human reference genome hg19 allowing for splicing alignment and using only uniquely aligned reads. Reads mapping to ribosomal RNAs, non-coding RNAs (Guttman et al., 2013) were then removed, and linkers used in library generation, incomplete and spurious alignments, and aligned lengths between 25 and 35 nucleotides (see methods) (FIG. 10A/B). The majority of the remaining reads now mapped to protein coding genes (FIG. 10C/D). The total number of RF reads that mapped to exons was 3.2 million in control and 3.4 million Silvestrol samples and this corresponded to ˜11,128 protein coding genes.

Silvestrol produced an immediate and broad inhibitory effect on cap-dependent translation. RF reads were fewer in number and showed a wider variation between control and silvestrol than total RNA sequences indicating minimal transcriptional variation (FIG. 10E). The number of ribosomes occupying a given transcript is given as gene specific RF reads per one million total reads (RPM). The RPM frequency distribution of control and silvestrol samples were overlapping, indicating that silvestrol equally affected mRNAs with high and low ribosome occupancy (FIG. 10F). Measurements of nascent protein synthesis with L-azidohomoalanine (AHA) labeling confirmed a broad inhibitory effect on translation (max. reduction with silvestrol ˜60%; p(Silv. vs. Veh.)=3.6×10−3, and 80% with cycloheximide, p(CHX vs. Veh.)=2×10−4) (FIG. 10G). Consistently, analyses of polyribosome bound RNA indicated loss of polyribosome bound RNA (fractions 30-40) upon silvestrol treatment (FIG. 10H).

Silvestrol affected the translational efficiency of specific sets of mRNAs. To calculate the translational efficiency (TE) for each mRNA the RF frequency was normalized to the length of the corresponding mRNA yielding an RF density (expressed as RPKM: reads per kilobase per million reads), and was corrected for total mRNA expression. Overall RPKM values for RF from vehicle and silvestrol treated samples were significantly correlated (R2=0.94) indicating a broad inhibitory effect on translation (FIG. 3B). The DERseq algorithm (Differential Expression-normalized Ribosome-occupancy) was used, based on the reported DEXseq algorithm (Anders et al., 2012), to identify mRNAs that were strongly affected by silvestrol (see method). A cut-off at p<0.03 (corresponding to a Z-score >2.5) was used to define groups of mRNAs whose translational efficiency (TE) was either most (TE down; red) or least (TE up; blue) affected by silvestrol compared to most other mRNAs (background; grey) (FIG. 3C, see also U.S. application Ser. No. 61/912,420, filed Dec. 5, 2013; and Wolfe A L, Singh K, Zhong Y, Drewe P, Rajasekhar V K, Sanghvi V R, Mavrakis K J, Jiang M, Roderick J E, Van der Meulen J, Schatz J H, Rodrigo C M, Zhao C, Rondou P, de Stanchina E, Teruya-Feldstein J, Kelliher M A, Speleman F, Porco J A Jr, Pelletier J, Ratsch G, Wendel H. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature. 2014 Sep. 4; 513(7516):65-70. doi: 10.1038/nature13485. Epub 2014 Jul. 27, both of which are incorporated herein by reference in their entireties) (Thoreen et al., 2012). The TE down group included 281 mRNAs (220 have annotated 5′UTRs), TE up included 190 mRNAs, and the background list included 2243 mRNAs. These groups were used to define the characteristics of differentially affected mRNAs.

FIG. 3 depicts transcriptome-scale ribosome footprinting defines silvestrol's effects on translation. A) Schematic of the ribosome footprinting experiments (see text for details). B) Ribosome density for transcripts across control and silvestrol samples (ribosomal footprint (RF) reads per kilobase per million reads (RPKM)). The correlation (R2=0.94) indicates a broad effect on translation and transcripts with significantly differential changes in ribosome density are indicated as red and blue dots. C) Frequency distribution of the ratio of translational efficiency (TE=foot print density corrected for total mRNA abundance) in control and silvestrol treated samples (TESilvestrol/TEcontrol). Red and blue areas indicate groups of more (TE down) or less (TE up) affected mRNAs with a cut-off at p<0.03; a second cut-off is indicated light blue/red for p<0.13). D) Comparison of 5′UTRs lengths for TE down versus background genes. Mathematical density is scaled such that all values on the x-axis sum to 1; red: TE down, black: background genes, *: mean value. E) Prevalence of the indicated 5′UTR motifs among the TE down and background genes. F) A consensus 12-mer motif enriched in the TE down genes. G) Illustration of base-pair interactions in a predicted G-quadruplex based on the sequence motif. H) Enrichment of predicted 5′UTR G-quadruplex structures in the TE down gene set (* indicates p<0.05). I) Venn diagram indicating the overlap of genes containing 12-mer motifs and G-quadruplexes in TE down genes. J) Schematic of the NDFIP1 5′UTR showing a G-quadruplex region matching the 12-mer (GGC)4 motif.

FIG. 10 depicts ribosome profiling quality control data and effects on translation. A and B) Read counts by length of mapped sequence before and after filtering rRNA, linker reads, non-coding RNAs, short mapped sequences (“noisy” reads; see text and method for details). C and D) Read length frequency histograms and mapping analysis of ribosome footprint data after quality control filtering for vehicle treated cells (C) or silvestrol treated cells (D). E) Silvestrol induced changes in total RNA (log 2 Fold change RPKM) and ribosome protected RNA (RF). F) Histogram of all genes' ribosome footprint intensity (measured as unique read number per million per gene, RPM) for silvestrol and vehicle treated cells indicating silvestrol affected mRNAs were broadly distributed (see text for details). G) Mean fluorescence intensity of incorporated L-azidohomoalanine (AHA) in newly synthesized proteins in KOPTK1 cells treated with vehicle (DMSO), silvestrol (Silv. 25 nM), or Cycloheximide (CHX 100 nM) for the indicated time period. H) Polyribosome profiles of silvestrol (25 nM) or vehicle (DMSO) treated KOPT-K1 cells showing OD254 absorption across the ribosome containing fractions. I) Length comparison of 5′UTRs of TE up genes and a background gene set; *: mean J) Percentage of TE up genes and background genes containing the indicated sequence motifs; *: p<0.001. K) Consensus logos showing the three most significant 9-mer motifs enriched in TE down genes. The TE up genes do not have a motif. L) Venn diagram indicating the overlap between genes containing 9-mers and G-quadruplexes in TE down genes.

Example 4 Hallmarks of eIF4A-Dependent and Silvestrol-Sensitive Transcripts

5′UTR length has been implicated in translational control (Hay and Sonenberg, 2004), although a recent study found no effects of UTR length on mTORC1-dependent translation (Thoreen et al., 2012). Comparing the 5′UTR length across TE up, TE down, and background groups (as described in U.S. application Ser. No. 61/912,420, filed Dec. 5, 2013; and Wolfe et al., Nature. 2014 Sep. 4; 513(7516):65-70), it was observed that mRNAs with longer 5′UTRs were significantly enriched among the most silvestrol-sensitive mRNAs (TE down: mean UTR length 368 nucleotides; background: mean 250 nucleotides; p(Silvestrol vs. Control)=7.6×10−12 using two-sample Kolmogorov-Smirnov) (FIG. 3D). On the other hand, the TE up group showed no significant difference in 5′UTR length (TE up: 265 nucleotides; p(Silvestrol vs. Control)=0.165) (FIG. 10I).

Known translation regulatory elements were sought. For example, TOP sequences (cytidine in pos. 2 followed by 4-14 pyrimidines) (Meyuhas, 2000), TOP-like sequences (cytidine in pos. 1-4 and >5 pyrimidines) (Thoreen et al., 2012), internal ribosome entry sites (IRES) (Pelletier and Sonenberg, 1988), and pyrimidine rich translational elements (PRTEs) (Meyuhas, 2000). Comparing TE down and the background lists no predilection was found for TOP, TOP-like, PRTE, or IRES elements (FIG. 3E). On the other hand, the TE up group showed a significant enrichment for IRES elements and this is consistent with the dual-luciferase reporter assay and previous characterization of IRES dependent translation (Bordeleau et al., 2006) (FIG. 10J; see also FIG. 2A, FIG. 9A).

Next it was sought to identify a sequence motif that might confer eIF4A dependence. The DREME algorithm was used to look for significantly enriched sequences in the TE down and TE up groups compared to the background list (as described in U.S. application Ser. No. 61/912,420, filed Dec. 5, 2013; and Wolfe et al., Nature. 2014 Sep. 4; 513(7516):65-70) (Bailey, 2011). No motif was found in the TE up group of mRNAs. However, the analysis revealed a 12-mer (GGC)₄ motif that was significantly over represented among the TE down transcripts and present in 94 out of 220 genes (p<2.2×10-16) (FIG. 3F, Table 3A). In addition, 14 shorter 9-mer motifs were found that were similarly enriched in the TE down group and occurred in 177 of 220 genes (p<4.2ex10-15) (Figure S3K, Table 3B). P-values were computed using a one-sided binomial test while accounting for the different 5′ UTR lengths. A significantly higher than expected number of motif occurrences than explained by the larger UTR lengths were found (p<2.2×10-16).

Whether silvestrol-sensitive mRNAs might have specific structural features that set them apart from less affected transcripts was considered. Using the program RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) the background, TE up, and TE down genes were modeled and a striking enrichment was observed for G-quadruplex structures among the TE down genes (p=2×10-11) (FIG. 3G-I). Specifically, 79 of the 220 TE down transcripts with annotated 5′UTRs harbored at least one G-quadruplex. Moreover, in 48 out of 79 transcripts, G-quadruplex structures perfectly co-localized with the (GGC)4 12-mer sequence motif (FIG. 31, Table 3C). Briefly, G-quadruplex structures are based on non-Watson-Crick interactions between at least four paired guanine nucleotides that align in different planes and are connected by at least one linker nucleotide (FIG. 3F/G) (Bugaut and Balasubramanian, 2012). Most often two guanines were observed separated by an intervening cytosine and sometimes an adenine (FIG. 3F). The NDFIP1 5′UTR exemplifies the folding and typical pattern observed, with more than one G-quadruplex and one that directly matches the 12-mer (GGC)4 motif and a second larger structure that is formed by a longer nucleotide sequence including elements that are similar although not identical to the canonical (GGC)4 motif (FIG. 3J). While a 9-mer sequence is insufficient to form the structure, these motifs are found to be highly enriched within G-quadruplex structures. For example, the most common 9-mer motif overlapped with G-quadruplex structures in 45% (p=2.2×10-6), the second most common in 21% (p=1.4×10-10). In these instances, nucleotides adjacent to the motif completed the structure (Table 4, illustrated in FIG. 11H). Together, these analyses indicate that long 5′UTRs and a (GGC)4 motif or highly similar sequence patterns that can form G-quadruplex structures are the hallmarks of eIF4A-dependent and silvestrol-sensitive translation.

FIG. 11 shows the analysis of genes with differential ribosomal distribution (rDiff positive set). A) Representation of ribosome coverage for all 847 transcripts with significant changes in distribution between silvestrol (red) and vehicle (black); corresponding to the rDiff positive gene list. Both RF coverage and transcript length are normalized for comparison; translation start and stop sites are indicated by blue lines. B-C) Ribosomal distribution plots as in A showing how silvestrol affects ribosome distribution in all TE up genes (B) and all TE down genes (C). D) Length comparison of 5′UTRs of genes with significantly altered ribosomal distribution (rDiff positive: red) and background genes (black); *: mean value. E) Percentage of rDiff positive genes and background genes containing the indicated sequence motifs.* indicates p<0.05. F-G) Venn diagrams indicating overlap between genes containing 12-mers (F) or 9-mers (G) and G-quadruplexes in rDiff positive genes. H) Schematic of the ADAM10 5′UTR with G-quadruplexes and indicating an example of a 9-mer sequence contributing to the G-quadruplex. I) Diagram of Renilla luciferase expressed from four G-quadruplexes in tandem (GQs, red) and Firefly luciferase expressed from the HCV IRES (white). J) Relative amounts of Renilla luciferase expressed from the GQ construct in 3T3 cells and normalized to IRES/Firefly with either empty vector or the indicated genes (* p<0.05). K) Relative amounts of Renilla luciferase expressed from the GQ construct in 3T3 cells and normalized to IRES/Firefly with either empty vector or the indicated genes, treated with silvestrol (25 nM) for 24 hours.

Example 5 Silvestrol Causes an Accumulation of RFs in the 5′UTR of Sensitive Transcripts

Next, the distribution of ribosomes was examined along the transcript as this might provide an additional indication of eIF4A sensitive translation (FIG. 4A). Note that the footprinting methodology provides exact sequence and positional information for each RF, and using the rDiff algorithm significant changes in read density were identified across the length of any given transcript (see method) (Drewe et al., 2013). A p-value cutoff of p<0.001 was used to identify a group (the rDiff positive set) of 847 protein-coding transcripts (641 with an annotated 5′UTR) that showed the most significant change in RF distribution (Table 5). These transcripts showed an accumulation in the 5′UTR and corresponding loss of coverage across the coding sequence. This silvestrol effect is most pronounced for the 62 genes that show decreased TE (TE down) and significant change in rDiff whereas it is absent in the TE up group (FIG. 4B, FIG. 11A-C, Table 6).

Similar to the TE down group an enrichment of longer 5′UTR in the rDiff positive set was found (rDiff pos.: n=641; mean length 271 nucleotides; Background (rDiff negative=no significant change): n=976, mean UTR length: 230 nucleotides; p=0.004) (Figure S4D). No significant enrichment for TOP, PRTE, or IRES elements was detected, however there was a small and significant drop in TOP-like sequences (Figure S4E). The DREME analysis for sequence motifs identified a significant enrichment for a 12-mer and three 9-mer motifs among rDiff positive genes (p=2.2×10-16) (FIG. 4C/D, Table 4, Table 7A/B). Among 641 genes in the rDiff group, the 12-mer motif occurred in 232, and an additional three 9-mer motifs were found in 322 genes. Notably, the motifs were nearly identical to the TE down motif (FIG. 3). Again, the 12-mer and 9-mer motifs co-localized to the majority of predicted G-quadruplexes observed in the rDiff positive gene set and this is illustrated with the ADAM10 5′UTR (FIG. 11F-H, Table 4, Table 7C). Hence, two different analyses—translation efficiency and RF distribution—point to the exact same patterns in eIF4A-sensitive transcripts: longer 5′UTRs with variations on the theme of a (GGC)4 sequence capable of G-quadruplex formation.

Next, directly testing the translational effect of the 12-mer sequence motif was sought. Briefly, a luciferase reporter system was constructed to directly compare four 12-mer motifs in tandem reflecting the common occurrence of multiple motifs in sensitive mRNAs (GQ construct) to a random sequence of equal length and GC content (control construct) and using an IRES-driven firefly luciferase as an internal control (FIG. 4E). First, treatment with silvestrol (25 nM) reduced the translation of the GQ construct and did not reduce the translation of the control luciferase. The RNA helicases DHX9 and DHX36 have been implicated in resolving G-quadruplex structures (Booy et al., 2012; Chakraborty and Grosse, 2011), however predominant expression was found of eIF4A in T-ALL (FIG. 4G) (Van Vlierberghe et al., 2011). Further direct testing was done of the effect of RNAi-mediated eIF4A knockdown in the same assay and a striking decrease in the translation from the GQ reporter observed, with little effect on the control sequence (FIG. 4H/I). Whether upstream activators or translation factors could enhance translation of the GQ construct was explored. It was found that only eIF4G could increase translation and that neither Akt, eIF4E, or eIF4A expression were sufficient (FIG. 11I/J). This is consistent with the notion that eIF4A levels are not limiting under physiological conditions and that additional factors (e.g. eIF4G) are needed for full eIF4A activation (Feoktistova et al., 2013; Oberer et al., 2005; Ozes et al., 2011). However, upon silvestrol treatment, it was observed that increased expression of wild type eIF4A or an RNA-binding site mutant protein (P159Q—homologous to S. cervesiae P147Q (Sadlish et al., 2013)) could render translation of the GQ reporter construct insensitive to silvestrol (FIG. 11K). Hence, pharmacologic and genetic evidence indicates that the 12-mer motif enriched in silvestrol sensitive transcripts requires eIF4A for translation.

FIG. 4 shows that silvestrol affects ribosome distribution in a subset of mRNAs. A) Diagram of differential ribosomal distribution along the length of a transcript. B) Representation of ribosome coverage for 62 TE down transcripts with changes in ribosomal distribution (rDiff positive); silvestrol (red), vehicle (black). RF coverage and transcript length are normalized for comparison, translation start and stop sites are indicated. C) rDiff positive genes were enriched for 9-mer and 12-mer motifs compared to background genes (* indicates p<0.05). D) The rDiff positive genes are enriched for the indicated 12-mer GC-rich consensus motif. E) Schematic of constructs expressing the indicated luciferase with 5′UTRs containing four 12-mer motifs in tandem (GQs, red), a random sequence matched for length and GC content (control, black), and the HCV IRES (white). F) Relative amounts of Renilla luciferase (normalized to Firefly) expressed from the GQs (red bars) or control construct (black bars), treated as indicated for 24 hours (* indicates p<0.05). G) Analysis of mRNA expression from (Van Vlierberghe et al., 2011) of the indicated RNA helicases in normal T-cells and T-ALL cells (* indicates p<0.05). H) Immunoblots of lysates from 3T3 cells with empty vector or sh-eIF4A and probed as indicated. I) Relative amounts of Renilla luciferase (normalized to Firefly) expressed from the GQs (red bars) or control construct (black bars), with empty vector or sh-eIF4A (* indicates p<0.05).

Example 6 Transcripts Affected by Silvestrol

The most silvestrol sensitive transcripts in the TE down group and the rDiff positive set include many genes with known roles in T-ALL (FIG. 5A/B). Categorization by gene ontology reveals a preponderance of transcription factors, many oncogenes, but also potential tumor suppressors (Figure S5A/5B). Sub-grouping of TE down genes by 5′UTR features (12-mer, 9-mer motif, and G-quadruplex structures) illustrates how sometimes multiple features occur in the same transcripts (Figure S5C-E). Exploring individual RF distribution graphs (normalized for mean RF count and gene length) illustrates recurrent patterns and also variations. For example, the c-MYC transcript (TE: p=1.3×10-4; rDiff: p=3×10-8) harbors six 9-mer motifs in its 5′UTR which correspond to peaks in RF density (FIG. 5C). Similarly, MDM2 (TE: p=0.94; rDIff: p=4.9×10-7) and RUNX1 (TE: p=4×10-3; rDIff: p=5.2×10-3) harbor multiple motifs and show a 5′UTR RF accumulation and drop across the coding region (FIG. 5D/E). CDK6 (TE: p=4×10-8; rDIff: p=4.7×10-5) shows the same pattern, and while the DREME analysis did not retrieve the typical motif it might harbor an alternate element (FIG. 5F). BCL2 (TE: p=8.6×10-3; rDIff: p=6.0×10-1), and BCL11B (TE: p=5.4×10-10; rDIff: p=1.0×10-8) have multiple 9-mer and 12-mer motifs and these transcripts show a drop in 5′UTR RF counts and peak shifts in their exonic regions (FIG. 5G/H). Several housekeeping genes have no recognizable motif and in particular actin shows no detectable effect of silvestrol on RF patterns (FIG. 5I-K).

FIG. 5 shows that many cancer genes are differentially affected by silvestrol. A) TE down genes in silvestrol treated KOPT-K1 ranked by translational efficiency (red, up to p=0.01). B) rDiff positive genes ranked by changes in ribosome distribution (up to p=0.001). C-K) Distribution of ribosomal footprints for the indicated genes. Silvestrol: Red; Vehicle: black; purple dots: 9-mer motifs; blue dots 12-mer motif.

FIG. 12 shows that gene ontology analysis of silvestrol sensitive genes. A) Number of genes in TE down group with G-quadruplex, 12-mer and 9-mer motif in the indicated gene family classifications. B) Number of genes in rDiff positive group with G-quadruplex, 12-mer and 9-mer motif in the indicated gene family classifications. C-E) Representative transcription factors and oncogenes with G-quadruplex (C), 12-mer (D), and 9-mer (E) motif in TE down genes, ranked by significant changes in translational efficiency.

Given the complexity of the RF data analysis, it was important to directly confirm loss of expression for at least some of these proteins. Briefly, immunoblots on JURKAT and KOPT-K1 cells treated with silvestrol (25 nM) and loaded with equal amounts of total protein confirmed dramatic loss of MYC, NOTCH1, BCL2, and CCND3 proteins (FIG. 6A). The effect on MYC was especially striking, it was dose dependent (FIG. 6B), lasted for 48 h, and was also achieved in xenografts in vivo (Figure S6A-B). Others whose expression was somewhat less decreased included MYB, CDK6, EZH2, and RUNX1/AML1. As expected, ACTIN, TUBULIN, and GAPDH were not affected (FIG. 6A). The same result was confirmed with the silvestrol analogue (CR) (Figure S6C). The effects were indeed posttranscriptional and no decrease was observed in the corresponding mRNA expression (FIG. 6C). The small and significant increase in MYC mRNA levels might be consistent with prior reports of a MYC auto-regulatory mechanism (Penn et al., 1990a; Penn et al., 1990b) (FIG. 6C).

Genomic studies have implicated many silvestrol-sensitive genes in T-ALL and other cancers. For example oncogenic mutations of NOTCH (Weng et al., 2004), increased CDK6/CCND3 (Sawai et al., 2012), and amplifications of MYB (Lahortiga et al., 2007) have been reported in T-ALL. Similarly, a brief survey of mRNA expression using RNAseq on 9 primary T-ALL samples compared to 4 T-cell samples confirms increased expression of NOTCH, MYB, CDK6, and BCL2 in T-ALL (FIG. 6D). Increased MYC activity has also been implicated in T-ALL (Gutierrez et al., 2011a; Palomero et al., 2006), and it was observed abundant MYC protein expression in ˜70% of T-ALLs by immunohistochemistry (Figure S6D). A direct tested was conducted on some of these genes for their role in T-ALL using the same mouse model described above (FIG. 1A). Briefly, Myb (n=4, p<0.0001), a mutant Ccnd3 (T283A) (n=5; p<0.0001), Bcl2 (n=4, p<0.0001), and p53 loss (as a surrogate for Mdm2; n=3; p<0.0001) accelerated leukemogenesis in the Notch context in vivo (FIG. 6E). However, silvestrol also affected candidate tumor suppressors in T-ALL, for example BCL11b (Gutierrez et al., 2011b), RUNX1 (Della Gatta et al., 2012; Giambra et al., 2012), and EZH2 (Ntziachristos et al., 2012). Direct testing of the effect of EZH2 knockdown (n=6, p<0.0001) demonstrated that EZH2 indeed acts as a tumor suppressor in T-ALL in vivo (FIG. 6E).

Given the pleiotropic effects of eIF4A inhibition it was considered which of its target genes may account for the drug's anti-leukemia effect. The MYC oncogene is a first candidate, because of silvestrol's powerful effects on MYC levels and its known oncogenic role in this cancer (Gutierrez et al., 2011a; Palomero et al., 2006). Moreover, genetic MYC blockade using the tamoxifen-inducible OmomycER allele (Soucek et al., 2008) readily induces cell death and clears T-ALL cells from the marrow leading to an extended survival in leukemic animals (nOMO=9, ncontrol=10; p=0.002) (FIG. 6F and inset). However, IRES-driven expression of MYC alone was unable to protect murine T-ALL cells from silvestrol. Similarly, IRES-driven expression of additional oncogenes including BCL2, NOTCH1, CCND3 (T283A) was not protective. Instead, cells expressing both IRES-MYC and IRES-BCL2 were significantly selected upon silvestrol treatment (FIG. 6G). These results suggest that silvestrol acts by disrupting the production of multiple pro-oncogenic multiple factors that are required to maintain the leukemia.

FIG. 6 depicts validation of selected silvestrol targets. A) Immunoblots of lysates from human T-ALL lines treated with silvestrol (25 nM) and probed as indicated. B) Immunoblots of lysates from JURKAT cells treated with escalating doses of silvestrol and probed as indicated. C) mRNA levels for the corresponding genes treated with vehicle (DMSO, black) or silvestrol (red, 25 nM); D) Volcano plot of mRNA expression changes of all TE Down and rDiff genes in T-ALL samples (n=9) compared to normal thymocytes (n=4). E) Kaplan-Meier analysis showing time to leukemia development (as in FIG. 1B). Wild-type HPCs transduced with NOTCH1-ICN and empty vector (black, n=14), Myb (red, n=4), Ccnd3 T283A (orange, n=5), or shEzh2 (orange, n=10), vavP-Bcl2 (brown, n=4), p53−/− (green, n=3). F) Effect of OmoMYCER activation on survival of leukemic animals; (d=0 represents start of therapy/tamoxifen (TAM) administration). Inset: clearance of GFP expressing murine T-ALL cells from the marrow upon OmomycER activation (Untr: untreated, TAM: tamoxifen). G) Competition experiment (as in FIG. 1C/D) showing the percentage of each starting GFP positive population of murine T-ALL cells partially transduced with the indicated constructs and treated with silvestrol (* indicates p<0.05).

FIG. 13 depicts the relative contribution of MYC and other silvestrol targets in T-ALL. A) Time course analysis of protein expression in KOPT-K1 cells treated with CR (25 nM) for the indicated number of hours. B) Immunoblot on CR or vehicle treated KOPT-K1 xenografts, probed as indicated. C) Immunoblots of lysates from human T-ALL lines treated with CR (25 nM, 24H) and probed as indicated. D) Representative section of tissue microarrays (TMA) representing 14 human T-ALLs and stained for MYC (lower panel) Scoring of the T-ALL MYC TMA: ‘0’=0%-25% positive cells, ‘1’=25%-75% positive cells, ‘2’=75%-100% positive cells. Normal spleen, kidney, and lymph node negative controls were present on the same slides. E) Histology from tamoxifen treated (50 mg/kg) xenografted T-ALL tumors expressing a control vector or OmomycER and stained as indicated. F-I) Immunoblots of lysates from murine T-ALL cells expressing either vector control or IRES-MYC (F), IRES-CCND3 T283A (G), IRES-ICN (H), or IRES-BCL2 (I) and probed as indicated.

Example 7 Study of G-Quadruplex Unwinding Mechanisms

A FRET-based assay was set up for measuring the effect of RNA helicases on G-quadruplex unwinding, screening proteins that can unwind G-quadruplexes and identify small molecules that stabilize the G-quadruplex structure. An RNA oligonucleotide (1XTEDownMotif 5′-UAGAA ACUAC GGCGG CGGCG GAAUC GUAGA; SEQ ID NO:65) containing the G-quadruplex motif was labeled with fluorophore FAM on the 5′ end and quencher BHQ1 on the 3′end. When folded, the labeled GQ RNA oligonucleotide will exhibit minimum baseline fluorescence. Addition of specific RNA helicase such as EIF4A with ATP and/or small molecules would result in unwinding and increase in fluorescence signal measured in real time, as shown in FIG. 14A.

FIG. 14B shows the optimization of fluorescence quenching assay using labeled RNA G-quadruplex oligonucleotide. Fluorescence was measured as function of concentration using G-quadruplex RNA with or without KCl. Without KCl fluorescence intensity increases as a function of concentration while in the presence of KCl it remains stable, suggesting the formation of a stable G-quadruplex structure in the presence of KCl.

Fluorescence measured as function of concentration using a mutant RNA (1XMutant; 5′-UAGACCCUGCAACGUCAGCGUAGUCGUAGC; SEQ ID NO:66) with or without KCl is shown in FIG. 14C. Fluorescence intensity increase as a function of concentration irrespective of KCl suggesting no particular secondary structure present in the mutant RNA oligonucleotide.

In FIG. 14D, the G-quadruplex versus mutant RNA oligonucleotide were compared using the fluorescence quenching assay. The fluorescence intensity of the G-quadruplex RNA remains stable and lower compared to the mutant RNA oligonucleotide. Mutant RNA shows an increase in fluorescence intensity as a function of concentration. Chemical unwinding using formamide results in increase of fluorescence intensity of both G-quadruplex and mutant RNA oligonucleotide.

This assay can therefore be used for the aforementioned purpose as well as various other purposes such as but not limited to 1) measuring the effect of known RNA helicases such as eIF4A, DHX9 or DHX36 on G-quadruplex unwinding; 2) investigating the effect of other cofactors/inhibitors required for eIF4A activity; 3) a screening method to identify other proteins that can unwind G-quadruplexes; and 4) identifying and establishing the effect of small molecules that stabilize the G-quadruplex structure.

Example 8 Sensitivity of Cancers to Silvestrol

The IC50 of silvestrol in several small cell lung cancer lines was evaluated. As shown in FIG. 15, low IC50s were observed in cell lines NCI-H211, NCI-H446, NCI-H2171, NCI-H82, NCI-H526, NCI-H196 and NCI-H889, indicating high sensitivity to silvestrol. The IC50 values are shown in the left figure and the individual viability curves are shown at the right.

A range of sensitivities from renal carcinoma lines ACHN, A498, CAKI-1, CAKI-2 to 786-O was demonstrated, as shown in FIG. 16.

In addition, IC50s of 2 to 20 nM have been obtained with neuroblastoma cell lines SKNAS, CLBGA, IMR32 and N206. Pancreatic cancer line PANC-1 show sensitivity to 20 nM silvestrol and a loss of KRAS expression.

In addition to the renal cell carcinoma and small cell lung cancer lines mentioned above, about 60 cancer cell lines were evaluated for silvestrol sensitivity as shown in FIG. 17. Cancers including T-ALL, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, and non-small cell lung cancer, as well as gastric cancer, pancreatic carcinoma, Ewing sarcoma and lung adenocarcinoma. FIG. 18, lower left panel, shows that MYC expression is not correlated with silvestrol sensitivity, indicating that MYC expression alone is not predictive of potential sensitivity of a tumor to silvestrol or other eIF4A inhibitor compounds as described herein, and indicates that the predictors of silvestrol sensitivity as described herein with the exclusion of MYC expression are useful for determining whether a patient's cancer will be sensitive to silvestrol.

Example 9 The Reporter Assay Determines Activity of Hippuristanol and Pateamine A

Using the dual-luciferase reporter assay described above, where renilla and firefly luciferase are either capped or under control of an internal ribosomal entry site (IRES) element, both hippuristanol and pateamine A were shown to preferentially block cap-dependent over IRES-dependent translation (FIG. 19).

Example 10 In Vitro Data on Silvestrol in Small Cell Lung Cancer

The in vitro activity of silvestrol was evaluated against a panel of small cell lung cancer cell lines, shown in FIG. 20A. In these cell lines, the effect of silvestrol on key target proteins MYC, EZH2 and cKit were determined (FIG. 20B, C). FIG. 21A shows the effect of silvestrol on H82 small cell lung cancer cells in the presence and absence of serum. FIG. 21B shows the effect of silvestrol alone and in combination with a proteasome inhibitor MG-132 against H82 small cell lung cancer cells and in FIG. 21C, the effects on key target proteins EZH2 and MYC.

Example 11 Effectiveness of Silvestrol in Neuroblastoma Cell Lines In Vitro

The effect of silvestrol on several neuroblastoma cell lines was evaluated. The results are shown in the table below.

Cells Silvestrol (IC50 nM) Description BE(1)N 2.52 N-MYC IMR32 2.86 N_MYC SKNCM 20.21 BE(2)C 47.83 N-MYC

Example 12 Identification of G-Quadruplexes in KRAS

As shown in the four annotated transcripts of KRAS in FIG. 22A with different and overlapping 5′UTRs, the minimal/common region of the 5′UTR has two G-quadruplexes (FIG. 22B). They have at least two and up to five G-quadruplex structures (FIG. 22C-F). FIG. 23A shows the Mfold structure of the NRAS 5′UTR, and FIG. 23B compares the KRAS and NRAS transcripts showing a similar density of G-quadruplexes, identifying KRAS as a potential silvestrol target.

Example 13 Effect of Silvestrol on KRAS Protein Levels in PANC1 Cells In Vitro

Similarly to that described in Example 8, silvestrol at 50 nM shows a loss of KRAS expression (FIG. 24A). KRAS has a long T_(1/2) compared to MYC, and therefore the effect is less pronounced. The in vitro activity of an S6 kinase inhibitor, rapamycin, silvestrol and combinations on PNAC1 and MiaPaca2 cells are shown in FIGS. 24B and 24C, respectively.

Example 14 In Vivo Activity of Silvestrol Against MiaPaca2 Xenografts

FIG. 25 shows the results in mice with MiaPaca2 xenografts when of 0.2 mg/kg silvestrol or vehicle was administered every other day from days 30-60 following tumor implantation. FIG. 25A shows the outcome using fluorescent imaging at 8 weeks; the excised tumors are shown in FIG. 25B; and the tumor volumes in FIG. 25C.

Example 15 In Vivo Activity of Silvestrol Against Small Cell Lung Cancer

FIG. 26 shows the results of a xenograft experiment using small cell lung cancer line NCI-H82 and silvestrol administration. The average tumor volumes and animal weights are shown in the top left and bottom left graphs, respectively, and the data legends corresponding to the animal groups and treatments (dose level, dose regimen and compounds) in the photographs and their legends at the right. In FIG. 27, the results from the same experiment using 0.2 mg/kg and 0.5 mg/kg silvestrol are plotted in the left graph, and the effect on key target proteins at different time points on the right.

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TABLE 1 Detailed summary of T-ALL patient mutations MYC NOTCH1 mutation IL7R mutation PTEN mutation + deletion Genetic ID translocat Nucleotide change Predicted prot. lesion Domain Nt chg. Prot. chg. Domain Nucleotide change Predicted prot. lesion subtype 1 t(8; 14) (q24; q11) — — heterozygous deletion Unknown 2 — c.7331_7332insCG (heterozygous) p.V2444fs*35 PEST — c.[738delGTT; 737_741insCCCGG] TAL/LMO (SIL-TAL) (heterozygous) p.P246fs*11 3 — c.7393delC (heterozygous) p.L2465fs*13 PEST — c.388C > T (homozygous) p.R130* TAL/LMO (SIL-TAL) c.[5023_5024delTT, 5022_025insCCC](het.) p.S1675fs*8 HD 4 — c.[7372delC; 7372_7374insGGT] (het.) PEST — heterozygous deletion exon 4-9 TAL/LMO p.L2458fs*21 HD (LMO2) c.4802T > C (heterozygous) p.L1601P 5 — c.4802T > C (heterozygous) p.L1601P HD — — HOXA (inv(7)) 6 — c.7510C > T (heterozygous) p.Q2504* PEST — — TLX3 7 — C.5229C_5230GinsAGATTCCCTTATGGGACC (heterozygous) JM — — Unknown 8 — C.4858_4864TACTACG > CCCGTCC (het.) HD — — TAL/LMO p.1620_1622YYG > PDR (LMO2) 9 — c.7504C > T (heterozygous) p.Q2502* PEST — — Unknown c.5036T > C (heterozygous) p.L1679P HD 10 — C.4748_4749insCCCCCCTTATAC (het.) PY — — Unknown p.P1583_E1584insPPYT 11 — c.[4749_4752delGGAG; 4748_4749insC] (het.) HD — — Unknown p.E1584del 12 — c.4732_4737delGTGGTG (heterozygous) HD — — TAL/LMO p.V1578 _V1579del PEST (LMO2) c.7462C > T (heterozygous) p.Q2488* 13 — c. [7545_7548delTGAG; PEST — — HOXA (CALM-AF10 7545_7546insCTTT; 7552_7553insGAGC] (het.) 14 — c.7318delG (heterozygous) p.P2439fs*39 PEST — — TLX3 C.4728_4729insTTTCTCTTG (het.) HD p.V1576_V1577insFLL 15 — c.7563G > A (heterozygous) p.W2521* PEST — — TLX3 16 — c.7462C > T (heterozygous) p.Q2488* PEST — — TAL/LMO c.5077T > A (heterozygous) p.C1693S HD (LMO2) 17 — c.4821_4822insGGATTC (heterozygous) HD — — TAL/LMO p.F1607 > LDS (LMO2) 18 — c.4802T > C (heterozygous) p.L1601P HD — — TLX3 19 — c.4781T > C (heterozygous) p.L1594P HD — — TLX1 20 — c.4782_4783insGCC (heterozygous) HD — — TAL/LMO p.L1594_R1595insP HD (SIL-TAL) 21 — c.4802T > A (heterozygous) p.L1601Q HD — — TLX1 22 — — C.758T > G p.V253G TM — Unknown 23 — — — c.697C > T (heterozygous) p.R233* TLX3 heterozygous deletion 24 — — c.749_750insCCCCAGCTTGGATAG TAL/LMO (heterozygous) p.G251fs*5 (LMO2) 25 — — — c.295G > T (heterozygous) p.E99* TAL/LMO (SIL-TAL) 26 — — — heterozygous deletion exon 1-3 TAL/LMO (LMO2) 27 — — — — HOXA (inv(7)) 28 — — — — HOXA (MLL) 29 — — — — HOXA (MLL) 30 — — — — TAL/LMO (SIL-TAL) 31 — — — — TAL/LMO (SIL-TAL) 32 — — — — TAL/LMO (SIL-TAL) 33 — — — — TLX3 34 — — — — TLX1 35 — — — — TLX1 36 — — — — Unknown

TABLE 2 In vivo toxicity study of (±)-CR-31-B 2A. Individual body and organ weights. Body Weight Liver Spleen Left Kidney Right Kidney Group Animal # (gm) (gm) (gm) (gm) (gm) Vehicle Female 1 16.093 0.810 0.060 0.117 0.137 Day 5 2 17.550 0.925 0.060 0.132 0.129 3 18.866 0.965 0.059 0.176 0.192 4 16.826 0.889 0.057 0.149 0.136 Mean 17.334 0.897 0.059 0.144 0.149 Std Dev 1.182 0.066 0.001 0.025 0.029 N 4 4 4 4 4 0.2 mg/kg Female 7 15.962 0.807 0.049 0.108 0.119 Day 5 8 17.217 0.969 0.070 0.133 0.125 9 17.463 0.914 0.086 0.138 0.135 10  16.078 0.843 0.064 0.125 0.125 Mean 16.680 0.883 0.067 0.126 0.126 Std Dev 0.770 0.072 0.015 0.013 0.007 N 4 4 4 4 4 % ChVh −3.8 −1.6 13.6 −12.5 −15.4 Vehicle Female 5 17.878 0.977 0.063 0.136 0.150 Day 19 6 16.845 0.969 0.062 0.118 0.124 Mean 17.362 0.973 0.063 0.127 0.137 Std Dev 0.730 0.006 0.001 0.013 0.018 N 2 2 2 2 2 0.2 mg/kg Female 11 18.769 1.111 0.081 0.111 0.137 Day 19 12 17.192 0.988 0.048 0.113 0.127 Mean 17.981 1.050 0.065 0.112 0.132 Std Dev 1.115 0.087 0.023 0.001 0.007 N 2 2 2 2 2 % ChVh 3.6 7.9 3.2 −11.8 −3.6 Liver Spleen Left Kidney Right Kidney Group Animal # (% body wt) (% body wt) (% body wt) (% body wt) Vehicle Female 1 5.03 0.37 0.85 0.85 Day 5 2 5.27 0.34 0.75 0.74 3 5.12 0.31 0.93 1.02 4 5.28 0.34 0.89 0.81 Mean 5.18 0.34 0.86 0.86 Std Dev 0.12 0.02 0.08 0.12 N 4 4 4 4 0.2 mg/kg Female 7 5.06 0.31 0.75 0.75 Day 5 8 5.63 0.41 0.77 0.73 9 5.23 0.49 0.79 0.77 10  5.24 0.40 0.78 0.78 Mean 5.29 0.40 0.77 0.76 Std Dev 0.24 0.07 0.02 0.02 N 4 4 4 4 % ChVh 2.1 17.6 −10.5 −11.6 Vehicle Female 5 5.46 0.35 0.84 0.84 Day 19 6 5.75 0.37 0.70 0.74 Mean 5.61 0.36 0.77 0.79 Std Dev 0.21 0.01 0.10 0.07 N 2 2 2 2 0.2 mg/kg Female 11  5.92 0.43 0.73 0.73 Day 19 12  5.75 0.28 0.66 0.74 Mean 5.84 0.36 0.70 0.74 Std Dev 0.12 0.11 0.05 0.01 N 2 2 2 2 % ChVh 4.1 0.0 −9.1 −6.3 2B. Individual hematology WBC NEUT LYM MONO EOS BASO Group Animal# K/uL K/uL K/uL K/uL K/uL K/uL NEUT % LYM % MONO % EOS % BASO % Vehicle Female 1 7.24 0.65 6.33 0.24 0.01 0.01 8.92 87.47 3.38 0.17 0.07 Day 5 2 7.44 1.00 6.30 0.10 0.02 0.01 13.43 84.72 1.41 0.27 0.17 3 6.38 0.75 5.50 0.11 0.01 0.01 11.83 86.13 1.69 0.23 0.11 4 4.52 0.72 3.76 0.03 0.00 0.00 15.88 83.26 0.68 0.11 0.07 Mean 6.40 0.78 5.47 0.12 0.01 0.01 12.52 85.40 1.79 0.20 0.11 Std Dev 1.33 0.15 1.20 0.09 0.01 0.01 2.92 1.81 1.14 0.07 0.05 N 4 4 4 4 4 4 4 4 4 4 4 0.2 mg/kg 7 4.78 1.05 3.64 0.08 0.00 0.00 21.94 76.21 1.77 0.01 0.07 Female 8 6.90 1.69 4.96 0.24 0.01 0.00 24.51 71.86 3.45 0.14 0.04 Day 5 9 4.98 1.40 3.49 0.09 0.00 0.00 28.20 70.06 1.74 0.00 0.00 10  6.96 1.70 5.13 0.12 0.01 0.00 24.44 73.76 1.70 0.10 0.00 Mean 5.91 1.46 4.31 0.13 0.01 0.00 24.77 72.97 2.17 0.06 0.03 Std Dev 1.19 0.31 0.86 0.07 0.01 0.00 2.58 2.63 0.86 0.07 0.03 N 4 4 4 4 4 4 4 4 4 4 4 % ChVh −7.7 87.2 −21.2 8.3 0.0 −100.0 97.8 −14.6 21.2 −70.0 −72.7 Vehicle Female 5 5.44 0.79 4.51 0.10 0.04 0.01 14.44 82.94 1.76 0.76 0.10 Day 19 6 8.68 1.12 7.43 0.09 0.03 0.01 12.85 85.63 1.06 0.34 0.11 Mean 7.06 0.96 5.97 0.10 0.04 0.01 13.65 84.29 1.41 0.55 0.11 Std Dev 2.29 0.23 2.06 0.01 0.01 0.00 1.12 1.90 0.49 0.30 0.01 N 2 2 2 2 2 2 2 2 2 2 2 0.2 mg/kg Female 11  3.36 0.51 2.80 0.03 0.02 0.00 15.03 83.42 0.91 0.50 0.14 Day 19 12  2.50 0.33 2.12 0.02 0.02 0.00 13.29 84.96 0.95 0.66 0.13 Mean 2.93 0.42 2.46 0.03 0.02 0.00 14.16 84.19 0.93 0.58 0.14 Std Dev 0.61 0.13 0.48 0.01 0.00 0.00 1.23 1.09 0.03 0.11 0.01 N 2 2 2 2 2 2 2 2 2 2 2 % ChVh −58.5 −56.3 −58.8 −70.0 −50.0 −100.0 3.7 −0.1 −34.0 5.5 27.3 RBC HGB MCV MCH MCHC PLT MPV Group Animal# M/uL g/dL HCT % fL Pg g/dL RDW % K/uL fL Vehicle Female 1 8.47 11.9 39.7 46.9 14.0 30.0 16.0 1343 4.6 Day 5 2 9.19 13.8 46.9 51.0 15.0 29.4 15.8 1097 4.7 3 8.51 13.1 44.3 52.0 15.4 29.6 16.3 839 4.4 4 8.97 13.5 45.4 50.6 15.1 29.7 15.6 809 4.3 Mean 8.79 13.1 44.1 50.1 14.9 29.7 15.9 1022.0 4.5 Std Dev 0.35 0.83 3.11 2.23 0.61 0.25 0.30 250.02 0.18 N 4 4 4 4 4 4 4 4 4 0.2 mg/kg 7 9.31 14.3 48.3 51.9 15.4 29.6 15.6 872 4.3 Female Day 5 8 8.95 13.8 45.1 50.4 15.4 30.6 16.1 673 4.3 9 8.69 13.0 43.9 50.5 15.0 29.6 15.2 676 4.1 10  8.89 13.5 45.0 50.6 15.2 30.0 16.4 682 4.3 Mean 8.96 13.7 45.6 50.9 15.3 30.0 15.8 725.8 4.3 Std Dev 0.26 0.54 1.90 0.70 0.19 0.47 0.53 97.57 0.10 N 4 4 4 4 4 4 4 4 4 % ChVh 1.9 4.4 3.4 1.4 2.5 0.9 −0.6 −29.0 −5.6 Vehicle Female 5 9.02 14.0 43.8 48.6 15.5 32.0 16.3 1216 4.7 Day 19 6 9.06 13.8 44.3 48.9 15.2 31.2 16.1 949 4.4 Mean 9.04 13.9 44.1 48.8 15.4 31.6 16.2 1082.5 4.6 Std Dev 0.03 0.14 0.35 0.21 0.21 0.57 0.14 188.80 0.21 N 2 2 2 2 2 2 2 2 2 0.2 mg/kg Female 11  9.33 13.4 45.9 49.2 14.4 29.2 16.4 990 4.6 Day 19 12  8.70 13.0 42.5 48.8 14.9 30.6 16.2 1403 4.9 Mean 9.02 13.2 44.2 49.0 14.7 29.9 16.3 1196.5 4.8 Std Dev 0.45 0.28 2.40 0.28 0.35 0.99 0.14 292.04 0.21 N 2 2 2 2 2 2 2 2 2 % ChVh −0.2 −5.0 0.2 0.4 -4.5 -5.4 0.6 10.5 4.3 2C. Bone marrow and spleen cytology Bone Marrow Mat % mat Pro % Pro Total % T Mat % Mat Prol % Pro Total % T Animal myel myel myel myel myel myel ery ery ery ery Ery ery Vehicle #1 124 41.3 28 9.3 152 50.7 57 19.0 29 9.7 86 28.7 Vehicle #2 121 40.3 30 10.0 151 50.3 64 21.3 24 8.0 88 29.3 Vehicle #3 105 35.0 58 19.3 163 54.3 57 19.0 32 10.7  89 29.7 Vehicle #4 115 38.3 46 15.3 161 53.7 47 15.7 26 8.7 73 24.3 Treatment #7 122 40.7 34 11.3 156 52.0 56 18.7 24 8.0 80 26.7 Treatment #8 88 29.3 64 21.3 152 50.7 62 20.7 26 8.7 88 29.3 Treatment #9 120 40.0 52 17.3 172 57.3 45 15.0 22 7.3 67 22.3 Treatment #10 121 40.3 72 24.0 193 64.3 38 12.7 25 8.3 63 21.0 Spleen Animal % Lymph % Macrophage % Myeloid % Erythroid % Plasma % Mesenchymal Vehicle #1 92 6 1 1 0 0 Vehicle #2 93 2 5 0 0 0 Vehicle #3 96 1 1 0 0 2 Vehicle #4 97 2 0 0 1 0 Treatment #7 94 2 4 0 0 0 Treatment #8 90 2 7 0 1 0 Treatment #9 90 0 9 1 0 0 Treatment #10 86 2 10  0 0 2 Mat Total Animal myel Lymph % Lymph Plasma % Plasma Mast % Mast Mega* Quality* cell M:E Vehicle #1 124 62 20.7 0 0.0 0 0.0 p a 300 1.8 Vehicle #2 121 61 20.3 0 0.0 0 0.0 p a 300 1.7 Vehicle #3 105 48 16.0 0 0.0 0 0.0 p a 300 1.8 Vehicle #4 115 66 22.0 0 0.0 0 0.0 P a 300 2.2 0.0 0.0 Treatment #7 122 64 21.3 0 0.0 0 0.0 P a 300 2.0 Treatment #8 88 60 20.0 0 0.0 0 0.0 p a 300 1.7 Treatment #9 120 61 20.3 0 0.0 0 0.0 p a 300 2.6 Treatment #10 121 44 14.7 0 0.0 0 0.0 300 3.1 Spleen Animal % Lymph Comment Total % Vehicle #1 92 100 Vehicle #2 93 100 Vehicle #3 96 100 Vehicle #4 97 large numbers of pleomorphic rod bacteria 100 in background of smear Treatment #7 94 100 Treatment #8 90 100 Treatment #9 90 100 Treatment #10 86 100 2D. Individual chemistry ALP ALT AST GGT ALB TP GLOB A/G TBIL BUN CRTN Group Animal # U/L U/L U/L U/L g/dL g/dL g/dL Ratio mg/d L mg/d L mg/dL Vehicle Female 1 125 22 39 0 2.8 4.5 1.7 1.6 0.2 24 0.1 Day 5 2 115 14 31 0 3.1 4.9 1.8 1.7 0.2 28 0.2 3 122 19 32 0 2.9 4.5 1.6 1.8 0.1 23 0.2 4 133 22 34 0 3.0 4.7 1.7 1.8 0.2 31 0.2 Mean 123.8 19.3 34.0 0.0 3.0 4.7 1.7 1.7 0.18 26.5 0.18 Std 7.46 3.77 3.56 0.00 0.13 0.19 0.08 0.10 0.05 3.70 0.05 Dev N 4 4 4 4 4 4 4 4 4 4 4 0.2 mg/kg 7 116 26 51 0 3.3 5.1 1.8 1.8 0.2 27 0.2 Female 8 114 20 35 0 3.0 4.8 1.8 1.7 0.2 26 0.2 Day 5 9 123 34 44 0 2.9 4.8 1.9 1.5 0.1 27 0.2 10  144 20 35 0 3.1 4.9 1.8 1.7 0.2 29 0.2 Mean 124.3 25.0 41.3 0.0 3.1 4.9 1.8 1.7 0.18 27.3 0.20 Std 13.72 6.63 7.76 0.00 0.17 0.14 0.05 0.13 0.05 1.26 0.00 Dev N 4 4 4 4 4 4 4 4 4 4 4 % ChVh 3.3 4.3 5.9 0.0 0.0 3.0 11.1 FoldChVh 1.0 1.3 1.2 NC Vehicle Female 5 164 20 46 0 3.2 5.1 1.9 1.7 0.1 31 0.2 Day 19 6 193 40 78 0 2.9 4.6 1.7 1.7 0.0 34 0.2 Mean 178.5 30.0 62.0 0.0 3.1 4.9 1.8 1.7 0.05 32.5 0.20 Std Dev 20.51 14.14 22.63 0.00 0.21 0.35 0.14 0.00 0.07 2.12 0.00 N 2 2 2 2 2 2 2 2 2 2 2 0.2 mg/kg Female 11  144 20 33 0 2.9 4.7 1.8 1.6 0.1 29 0.2 Day 19 12  160 22 38 0 2.9 4.7 1.8 1.6 0.1 35 0.2 Mean 152.0 21.0 35.5 0.0 2.9 4.7 1.8 1.6 0.10 32.0 0.20 Std 11.31 1.41 3.54 0.00 0.00 0.00 0.00 0.00 0.00 4.24 0.00 Dev N 2 2 2 2 2 2 2 2 2 2 2 % ChVh -6.5 -4.1 0.0 -5.9 100.0 -1.5 0.0 FoldChVh 0.9 0.7 0.6 NC Animal CHOL GLUC Ca P Cl K Na Na/K Group # mg/dL mg/dL mg/dL mg/dL mEq/L mEq/L mEq/L Ratio Vehicle Female 1 62 301 7.1 8.1 113 5.7 148 26 Day 5 2 78 287 9.8 7.3 113 3.8 150 39 3 63 307 9.5 7.5 116 4.0 151 38 4 61 273 9.2 9.8 111 4.0 148 37 Mean 66.0 292.0 8.9 8.2 113.3 4.4 149.3 35.0 Std Dev 8.04 15.19 1.22 1.14 2.06 0.89 1.50 6.06 N 4 4 4 4 4 4 4 4 7 68 270 8.9 6.3 116 4.6 152 33 0.2 mg/kg Female 8 66 335 9.0 7.3 113 4.0 147 37 Day 5 9 64 261 9.3 7.5 114 4.4 150 34 10  66 323 9.3 7.0 113 3.9 147 38 Mean 66.0 297.3 9.1 7.0 114.0 4.2 149.0 35.5 Std Dev 1.63 37.17 0.21 0.53 1.41 0.33 2.45 2.38 N 4 4 4 4 4 4 4 4 % ChVh 0.0 1.8 2.2 −14.6 0.6 −4.5 −0.2 1.4 FoldChVh Vehicle Female 5 74 261 9.4 6.0 116 4.3 148 34 Day 19 6 59 261 9.5 7.5 116 4.1 148 36 Mean 66.5 261.0 9.5 6.8 116.0 4.2 148.0 35.0 Std Dev 10.61 0.00 0.07 1.06 0.00 0.14 0.00 1.41 N 2 2 2 2 2 2 2 2 0.2 mg/kg Female 11  71 254 9.0 9.6 112 3.5 147 42 Day 19 12  59 227 9.4 10.8 117 4.0 149 37 Mean 65.0 240.5 9.2 10.2 114.5 3.8 148.0 39.5 Std Dev 8.49 19.09 0.28 0.85 3.54 0.35 1.41 3.54 N 2 2 2 2 2 2 2 2 % ChVh −2.3 −7.9 −3.2 50.0 −1.3 −9.5 0.0 12.9 FoldChVh *p = present a = adequate

TABLE 3A Motifs and G-quadruplexes in TE down genes. Gene ID Gene Name Translational Efficiency (p-value) log2 (Translational Efficiency) rDiff (p-value) ENSG00000204147 ASAH2B 0.015002357 −1.322460998 1 ENSG00000125827 TMX4 0.004516727 −1.251223509 1 ENSG00000008710 PKD1 0.016462045 −1.049712325 1 ENSG00000182197 EXT1 0.024702029 −0.999952768 1 ENSG00000181027 FKRP 0.016390601 −0.996001717 1 ENSG00000056998 GYG2 0.026501722 −0.929650779 1 ENSG00000124786 SLC35B3 0.023814954 −0.917840885 1 ENSG00000164970 FAM219A 0.012381128 −0.63799892  1 ENSG00000065802 ASB1 0.011120438 −0.632831228 7.24E−02 ENSG00000150995 ITPR1 0.025529346 −0.628260516 1 ENSG00000130669 PAK4 0.02752902 −0.627975797 1 ENSG00000166503 HDGFRP3 0.000273828 −0.608750084 1.19E−02 ENSG00000180730 SHISA2 2.85E−05 −0.608613867 1.93E−02 ENSG00000119844 AFTPH 0.008725735 −0.591675727 1 ENSG00000180035 ZNF48 0.015918146 −0.582772982 1 ENSG00000133056 PIK3C2B 0.016052253 −0.537952135 1 ENSG00000109220 CHIC2 0.018242688 −0.521221308 1.70E−02 ENSG00000127152 BCL11B 5.40E−10 −0.517770746 1.00E−08 ENSG00000140853 NLRC5 0.009461003 −0.515280789 1 ENSG00000034677 RNF19A 0.025744017 −0.483894067 1 ENSG00000105321 CCDC9 0.020946401 −0.480466187 1 ENSG00000151014 CCRN4L 0.007814184 −0.480208055 7.50E−03 ENSG00000123159 GIPC1 0.00645275 −0.478285755 6.90E−03 ENSG00000171791 BCL2 0.008656918 −0.474172722 6.00E−01 ENSG00000065970 FOXJ2 0.017646559 −0.4735107   1 ENSG00000066933 MYO9A 0.008868511 −0.473506657 1 ENSG00000182150 ERCC6L2 0.016924169 −0.466789648 1 ENSG00000100393 EP300 1.18E−05 −0.464539688 1.10E−03 ENSG00000120949 TNFRSF8 0.022812631 −0.437286644 7.40E−03 ENSG00000123575 FAM199X 0.029642368 −0.431235143 2.08E−02 ENSG00000179195 ZNF664 0.005477293 −0.42685597  1 ENSG00000166024 R3HCC1L 0.024332543 −0.416140766 1 ENSG00000123066 MED13L 4.79E−05 −0.415941737 2.20E−08 ENSG00000145349 CAMK2D 0.021359574 −0.408237368 7.82E−02 ENSG00000110218 PANX1 0.005542647 −0.39874583  2.59E−02 ENSG00000003402 CFLAR 0.024657096 −0.397685039 4.71E−02 ENSG00000164168 TMEM184C 0.015050183 −0.397412646 2.50E−08 ENSG00000169018 FEM1B 0.01910054 −0.397020738 3.00E−04 ENSG00000007168 PAFAH1B1 0.000466042 −0.383179082 9.80E−03 ENSG00000169967 MAP3K2 0.013056576 −0.377048905 6.60E−03 ENSG00000162889 MAPKAPK2 0.016286083 −0.352699883 5.49E−01 ENSG00000063978 RNF4 0.002157553 −0.344201177 1.28E−02 ENSG00000064490 RFXANK 0.015800837 −0.324746409 3.00E−04 ENSG00000100105 PATZ1 0.00652701 −0.324460116 3.10E−03 ENSG00000103502 CDIPT 0.021406946 −0.323954264 1.43E−01 ENSG00000095380 NANS 0.027123309 −0.321819229 5.39E−02 ENSG00000160917 CPSF4 0.016200762 −0.319405125 1.70E−03 ENSG00000153561 RMND5A 0.029110593 −0.311729374 2.03E−01 ENSG00000108510 MED13 0.005034555 −0.293870753 1.60E−03 ENSG00000112531 QKI 0.00269178 −0.29125342  8.40E−03 ENSG00000163349 HIPK1 0.020020123 −0.282659771 2.00E−04 ENSG00000111885 MAN1A1 0.010654006 −0.274580872 2.24E−02 ENSG00000048405 ZNF800 0.020652909 −0.271097499 3.00E−08 ENSG00000115419 GLS 0.000197719 −0.269875671 4.00E−04 ENSG00000182831 C16orf72 0.00375696 −0.255255837 1.07E−01 ENSG00000131507 NDF1P1 0.004173323 −0.242895723 6.80E−03 ENSG00000134602 MST4 0.003080229 −0.242407773 1.05E−02 ENSG00000159692 CTBP1 0.006057739 −0.241648156 5.00E−03 ENSG00000106609 TMEM248 0.005316307 −0.23621242  2.90E−07 ENSG00000152684 PELO 0.01293572 −0.236131973 7.82E−02 ENSG00000134954 ETS1 1.27E−05 −0.232324455 5.70E−09 ENSG00000140332 TLE3 0.001343794 −0.227829431 2.00E−08 ENSG00000169905 TOR1AIP2 0.025144824 −0.223803399 7.00E−04 ENSG00000149480 MTA2 2.64E−05 −0.22354576  6.00E−09 ENSG00000105329 TGFB1 0.015301045 −0.221315351 2.00E−04 ENSG00000131504 DIAPH1 0.005406879 −0.213577391 2.00E−04 ENSG00000138795 LEF1 1.60E−06 −0.210659864 1.00E−09 ENSG00000106290 TAF6 0.014175182 −0.210235711 5.00E−04 ENSG00000137845 ADAM10 0.012053048 −0.208903322 9.00E−10 ENSG00000136878 USP20 0.019165529 −0.206602358 2.00E−08 ENSG00000172292 CERS6 0.029552171 −0.205124483 1.00E−09 ENSG00000135932 CAB39 0.019948395 −0.200243436 1.00E−08 ENSG00000118816 CCNI 0.001528498 −0.189161037 6.90E−07 ENSG00000151465 CDC123 0.007301 −0.184803611 3.23E−01 ENSG00000140262 TCF12 0.025334533 −0.184064816 2.00E−10 ENSG00000100796 SMEK1 0.021404696 −0.176469607 1.00E−11 ENSG00000112306 RPS12 0.029227861 −0.173199482 1.13E−01 ENSG00000105063 PPP6R1 0.029786388 −0.157573098 1.00E−10 ENSG00000120727 PAIP2 0.010801093 −0.157320231 5.59E−01 ENSG00000152601 MBNL1 0.00777836 −0.152181062 2.00E−11 ENSG00000088325 TPX2 0.000751758 −0.147886462 4.00E−13 ENSG00000171310 CHST11 0.004536717 −0.14604981  1.20E−07 ENSG00000158985 CDC42SE2 0.027991366 −0.145160094 8.00E−08 ENSG00000184007 PTP4A2 0.00039459 −0.142942918 1.50E−07 ENSG00000153310 FAM49B 0.007506383 −0.139159484 2.00E−04 ENSG00000121083 DYNLL2 0.02989098 −0.137797441 1.00E−03 ENSG00000078369 GNB1 0.011642786 −0.133797709 5.00E−04 ENSG00000125743 SNRPD2 0.024903253 −0.131448444 2.38E−01 ENSG00000110651 CD81 0.010480682 −0.130640591 1.00E−04 ENSG00000077312 SNRPA 0.023537735 −0.127819876 1.26E−01 ENSG00000125970 RALY 0.004001428 −0.112279678 3.64E−02 ENSG00000169764 UGP2 0.027598388 −0.103615488 1.60E−03 ENSG00000138668 HNRNPD 0.003261874 −0.098862205 2.40E−07 ENSG00000167978 SRRM2 0.027585188 −0.081656945 1.00E−04

TABLE 3B TE Down genes with 9-mer GC-rich motif Gene ID Gene Name Translational Efficiency (p-value) log2 (Translational Efficiency) rDiff (p-value) ENSG00000142530 FAM71E1 0.007231579 −13.06577528 1 ENSG00000164877 MICALL2 0.00343177 −13.04340083 1 ENSG00000205002 AARD 0.005983799 −12.57393172 1 ENSG00000096264 NCR2 0.004901353 −12.43253148 1 ENSG00000104881 PPP1R13L 0.01002069 −1.405330178 1 ENSG00000154016 GRAP 0.010299775 −1.388227224 1 ENSG00000025434 NR1H3 0.009825261 −1.378487187 1 ENSG00000204147 ASAH2B 0.015002357 −1.322460998 1 ENSG00000111664 GNB3 0.016841552 −1.309465795 1 ENSG00000154783 FGD5 0.010083869 −1.258941532 1 ENSG00000125827 TMX4 0.004516727 −1.251223509 1 ENSG00000139112 GABARAPL1 0.008844095 −1.233522978 1 ENSG00000162065 TBC1D24 0.005127762 −1.23071089  1 ENSG00000102265 TIMP1 0.019522742 −1.114778075 1 ENSG00000008710 PKD1 0.016462045 −1.049712325 1 ENSG00000182986 ZNF320 0.027309984 −1.003743356 1 ENSG00000106829 TLE4 0.000832033 −1.003696096 1 ENSG00000182197 EXT1 0.024702029 −0.999952768 1 ENSG00000181027 FKRP 0.016390601 −0.996001717 1 ENSG00000064687 ABCA7 0.01073148 −0.991801368 1 ENSG00000056998 GYG2 0.026501722 −0.929650779 1 ENSG00000124786 SLC35B3 0.023814954 −0.917840885 1 ENSG00000075399 VPS9D1 0.01039008 −0.829631073 1 ENSG00000172732 MUS81 0.000200214 −0.721332975 1.05E−01 ENSG00000055208 TAB2 0.005417389 −0.647025741 1 ENSG00000164970 FAM219A 0.012381128 −0.63799892  1 ENSG00000065802 ASB1 0.011120438 −0.632831228 7.24E−02 ENSG00000150995 ITPR1 0.025529346 −0.628260516 1 ENSG00000130669 PAK4 0.02752902 −0.627975797 1 ENSG00000112394 SLC16A10 0.018925329 −0.615544597 1 ENSG00000166503 HDGFRP3 0.000273828 −0.608750084 1.19E−02 ENSG00000180730 SHISA2 2.85E−05 −0.608613867 1.93E−02 ENSG00000176994 SMCR8 0.003428912 −0.604582332 1 ENSG00000204348 DOM3Z 0.026501738 −0.595853393 1 ENSG00000152127 MGAT5 0.000966439 −0.592236096 1.04E−01 ENSG00000119844 AFTPH 0.008725735 −0.591675727 1 ENSG00000180035 ZNF48 0.015918146 −0.582772982 1 ENSG00000132879 FBXO44 0.011714393 −0.538058958 1.10E−01 ENSG00000133056 PIK3C2B 0.016052253 −0.537952135 1 ENSG00000137822 TUBGCP4 0.017824276 −0.534568492 3.06E−02 ENSG00000109220 CHIC2 0.018242688 −0.521221308 1.70E−02 ENSG00000127152 BCL11B 5.40E−10 −0.517770746 1.00E−08 ENSG00000140853 NLRC5 0.009461003 −0.515280789 1 ENSG00000135049 AGTPBP1 0.005676581 −0.500916234 1 ENSG00000141873 SLC39A3 0.00107034 −0.49572766 1 ENSG00000034677 RNF19A 0.025744017 −0.483894067 1 ENSG00000105321 CCDC9 0.020946401 −0.480466187 1 ENSG00000151014 CCRN4L 0.007814184 −0.480208055 7.50E−03 ENSG00000123159 GIPC1 0.00645275 −0.478285755 6.90E−03 ENSG00000102384 CENPI 0.021332262 −0.475386617 5.97E−02 ENSG00000171791 BCL2 0.008656918 −0.474172722 6.00E−01 ENSG00000065970 FOXJ2 0.017646559 −0.4735107   1 ENSG00000066933 MYO9A 0.008868511 −0.473506657 1 ENSG00000120709 FAM53C 0.016598125 −0.471476024 2.15E−01 ENSG00000182150 ERCC6L2 0.016924169 −0.466789648 1 ENSG00000100393 EP300 1.18E−05 −0.464539688 1.10E−03 ENSG00000143479 DYRK3 0.013602392 −0.462587869 3.58E−02 ENSG00000136770 DNAJC1 0.019563299 −0.448209599 2.70E−03 ENSG00000100354 TNRC6B 0.002839187 −0.444181516 1 ENSG00000120949 TNFRSF8 0.022812631 −0.437286644 7.40E−03 ENSG00000154370 TRIM11 0.010190424 −0.431525912 3.01E−04 ENSG00000111450 STX2 0.024088299 −0.4313432   3.52E−01 ENSG00000123575 FAM199X 0.029642368 −0.431235143 2.08E−02 ENSG00000179195 ZNF664 0.005477293 −0.42685597  1 ENSG00000165244 ZNF367 0.002786549 −0.420795786 5.50E−03 ENSG00000166024 R3HCC1L 0.024332543 −0.416140766 1 ENSG00000123066 MED13L 4.79E−05 −0.415941737 2.20E−08 ENSG00000198924 DCLRE1A 0.011556077 −0.415137858 1.40E−02 ENSG00000143570 SLC39A1 0.002068007 −0.414472027 1.43E−01 ENSG00000145349 CAMK2D 0.021359574 −0.408237368 7.82E−02 ENSG00000110218 PANX1 0.005542647 −0.39874583  2.59E−02 ENSG00000003402 CFLAR 0.024657096 −0.397685039 4.71E−02 ENSG00000164168 TMEM184C 0.015050183 −0.397412646 2.50E−08 ENSG00000169018 FEM1B 0.01910054 −0.397020738 3.00E−04 ENSG00000168092 PAFAH1B2 0.008647229 −0.388340708 3.82E−02 ENSG00000178209 PLEC 0.015088771 −0.385965026 1 ENSG00000007168 PAFAH1B1 0.000466042 −0.383179082 9.80E−03 ENSG00000179912 R3HDM2 0.018146798 −0.377340675 9.00E−02 ENSG00000169967 MAP3K2 0.013056576 −0.377048905 6.60E−03 ENSG00000157600 TMEM164 0.010364528 −0.374375608 3.56E−01 ENSG00000213654 GPSM3 0.018261413 −0.371438487 1.02E−01 ENSG00000137310 TCF19 0.006852109 −0.371039482 2.27E−02 ENSG00000126215 XRCC3 0.022817606 −0.355664276 1.50E−03 ENSG00000033170 FUT8 0.006226232 −0.355628717 6.00E−04 ENSG00000162889 MAPKAPK2 0.016286083 −0.352699883 5.49E−01 ENSG00000063978 RNF4 0.002157553 −0.344201177 1.28E−02 ENSG00000177542 SLC25A22 0.013143394 −0.338628583 1.17E−01 ENSG00000132388 UBE2G1 0.000234936 −0.336746882 6.21E−03 ENSG00000170340 B3GNT2 0.004125239 −0.332264603 2.00E−02 ENSG00000064490 RFXANK 0.015800837 −0.324746409 3.00E−04 ENSG00000100105 PATZ1 0.00652701 −0.324460116 3.10E−03 ENSG00000103502 CDIPT 0.021406946 −0.323954264 1.43E−01 ENSG00000095380 NANS 0.027123309 −0.321819229 5.39E−02 ENSG00000160917 CPSF4 0.016200762 −0.319405125 1.70E−03 ENSG00000158435 CNOT11 0.001841931 −0.314941827 8.69E−02 ENSG00000153561 RMND5A 0.029110593 −0.311729374 2.03E−01 ENSG00000102858 MGRN1 0.02977034 −0.309624822 1.40E−02 ENSG00000058668 ATP2B4 0.000680955 −0.302809666 1.00E−09 ENSG00000143418 CERS2 5.25E−06 −0.30206333  2.77E−01 ENSG00000089009 RPL6 0.004810696 −0.297683768 3.87E−01 ENSG00000196155 PLEKHG4 0.015595222 −0.295432913 1.00E−04 ENSG00000108510 MED13 0.005034555 −0.293870753 1.60E−03 ENSG00000112531 QKI 0.00269178 −0.29125342  8.40E−03 ENSG00000053770 AP5M1 0.011896453 −0.283753407 1.00E−02 ENSG00000163349 HIPK1 0.020020123 −0.282659771 2.00E−04 ENSG00000122257 RBBP6 0.000891329 −0.280964053 1.25E−09 ENSG00000017483 SLC38A5 0.015966238 −0.280122734 2.30E−03 ENSG00000171522 PTGER4 0.002288634 −0.274827847 2.40E−07 ENSG00000111885 MAN1A1 0.010654006 −0.274580872 2.24E−02 ENSG00000048405 ZNF800 0.020652909 −0.271097499 3.00E−08 ENSG00000115419 GLS 0.000197719 −0.269875671 4.00E−04 ENSG00000112851 E RBB2IP 0.005962767 −0.26900197  3.00E−04 ENSG00000105287 PRKD2 0.018773736 −0.262403451 1.25E−02 ENSG00000182831 C16or172 0.00375696 −0.255255837 1.07E−01 ENSG00000007968 E2F2 0.009479782 −0.24865366  4.20E−03 ENSG00000100225 FBXO7 0.00882935 −0.246942196 1.08E−02 ENSG00000171552 BCL2L1 0.00522943 −0.245325394 6.32E−02 ENSG00000131507 NDFIP1 0.004173323 −0.242895723 6.80E−03 ENSG00000090621 PABPC4 0.000282201 −0.242834811 1.71E−02 ENSG00000134602 MST4 0.003080229 −0.242407773 1.05E−02 ENSG00000159692 CTBP1 0.006057739 −0.241648156 5.00E−03 ENSG00000133657 ATP13A3 0.021301072 −0.237052311 1.00E−10 ENSG00000106609 TMEM248 0.005316307 −0.23621242  2.90E−07 ENSG00000152684 PELO 0.01293572 −0.236131973 7.82E−02 ENSG00000104325 DECR1 0.01371001 −0.232829844 1.19E−02 ENSG00000134954 ETS1 1.27E−05 −0.232324455 5.70E−09 ENSG00000140332 TLE3 0.001343794 −0.227829431 2.00E−08 ENSG00000147140 NONO 0.003389405 −0.227308156 3.57E−02 ENSG00000169905 TOR1AIP2 0.025144824 −0.223803399 7.00E−04 ENSG00000149480 MTA2 2.64E−05 −0.22354576  6.00E−09 ENSG00000136997 MYC 0.000130485 −0.222358961 3.00E−08 ENSG00000105329 TGFB1 0.015301045 −0.221315351 2.00E−04 ENSG00000107485 GATA3 0.025270056 −0.218676008 1.34E−02 ENSG00000171858 RPS21 0.00024084 −0.216003759 5.41E−03 ENSG00000131504 DIAPH1 0.005406879 −0.213577391 2.00E−04 ENSG00000138795 LEF1 1.60E−06 −0.210659864 1.00E−09 ENSG00000106290 TAF6 0.014175182 −0.210235711 5.00E−04 ENSG00000137845 ADAM10 0.012053048 −0.208903322 9.00E−10 ENSG00000136878 USP20 0.019165529 −0.206602358 2.00E−08 ENSG00000174579 MSL2 0.027763257 −0.205275001 5.00E−04 ENSG00000172292 CERS6 0.029552171 −0.205124483 1.00E−09 ENSG00000125691 RPL23 0.004476603 −0.201854357 1.43E−02 ENSG00000135932 CAB39 0.019948395 −0.200243436 1.00E−08 ENSG00000155508 CNOT8 0.026465866 −0.200101165 6.78E−02 ENSG00000108578 BLMH 0.011959202 −0.198123991 1.66E−01 ENSG00000118816 CCNI 0.001528498 −0.189161037 6.90E−07 ENSG00000101972 STAG2 0.001047325 −0.187270211 7.00E−04 ENSG00000151465 CDC123 0.007301 −0.184803611 3.23E−01 ENSG00000140262 TCF12 0.025334533 −0.184064816 2.00E−10 ENSG00000159216 RUNX1 0.004534671 −0.177621274 5.20E−03 ENSG00000100796 SMEK1 0.021404696 −0.176469607 1.00E−11 ENSG00000143889 HNRPLL 0.02829111 −0.174975752 1.60E−03 ENSG00000112306 RPS12 0.029227861 −0.173199482 1.13E−01 ENSG00000108424 KPNB1 8.66E−05 −0.171777065 2.00E−11 ENSG00000085117 CD82 0.001401537 −0.168060459 2.70E−03 ENSG00000111371 SLC38A1 0.006852608 −0.165827185 3.43E−02 ENSG00000099800 TIMM13 0.01109652 −0.165570746 8.64E−02 ENSG00000105063 PPP6R1 0.029786388 −0.157573098 1.00E−10 ENSG00000120727 PAIP2 0.010801093 −0.157320231 5.59E−01 ENSG00000109685 WHSC1 0.0222009 −0.153361985 1.00E−11 ENSG00000152601 MBNL1 0.00777836 −0.152181062 2.00E−11 ENSG00000197771 MCMBP 0.0158736 −0.149779012 5.90E−03 ENSG00000088325 TPX2 0.000751758 −0.147886462 4.00E−13 ENSG00000171310 CHST11 0.004536717 −0.14604981  1.20E−07 ENSG00000158985 CDC42SE2 0.027991366 −0.145160094 8.00E−08 ENSG00000184007 PTP4A2 0.00039459 −0.142942918 1.50E−07 ENSG00000153310 FAM49B 0.007506383 −0.139159484 2.00E−04 ENSG00000121083 DYNLL2 0.02989098 −0.137797441 1.00E−03 ENSG00000078369 GNB1 0.011642786 −0.133797709 5.00E−04 ENSG00000125743 SNRPD2 0.024903253 −0.131448444 2.38E−01 ENSG00000110651 CD81 0.010480682 −0.130640591 1.00E−04 ENSG00000077312 SNRPA 0.023537735 −0.127819876 1.26E−01 ENSG00000125970 RALY 0.004001428 −0.112279678 3.64E−02 ENSG00000186468 RPS23 0.008328741 −0.104395342 5.03E−01 ENSG00000169764 UGP2 0.027598388 −0.103615488 1.60E−03 ENSG00000138668 HNRNPD 0.003261874 −0.098862205 2.40E−07 ENSG00000167978 SRRM2 0.027585188 −0.081656945 1.00E−04

TABLE 3C TE down genes with G-Quadruplex structure Gene ID Gene Name Translational Efficiency (p-value) log2(Translational Efficiency) rDiff (p-value) ENSG00000127152 BCL11B 5.40E−10 −0.517770746 1.00E−08 ENSG00000100393 EP300 1.18E−05 −0.464539688 1.10E−03 ENSG00000149480 MTA2 2.64E−05 −0.22354576 6.00E−09 ENSG00000180730 SHISA2 2.85E−05 −0.608613867 1.93E−02 ENSG00000123066 MED13L 4.79E−05 −0.415941737 2.20E−08 ENSG00000132388 UBE2G1 0.000234936 −0.336746882 6.21E−03 ENSG00000166503 HDGFRP3 0.000273828 −0.608750084 1.19E−02 ENSG00000090621 PABPC4 0.000282201 −0.242834811 1.71E−02 ENSG00000184007 PTP4A2 0.00039459 −0.142942918 1.50E−07 ENSG00000007168 PAFAH1B1 0.000466042 −0.383179082 9.80E−03 ENSG00000058668 ATP2B4 0.000680955 −0.302809666 1.00E−09 ENSG00000101972 STAG2 0.001047325 −0.187270211 7.00E−04 ENSG00000109654 TRIM2 0.001320775 −2.146623909 1 ENSG00000140332 TLE3 0.001343794 −0.227829431 2.00E−08 ENSG00000063978 RNF4 0.002157553 −0.344201177 1.28E−02 ENSG00000171522 PTGER4 0.002288634 −0.274827847 2.40E−07 ENSG00000112531 QKI 0.00269178 −0.29125342 8.40E−03 ENSG00000100354 TNRC6B 0.002839187 −0.444181516 1 ENSG00000182831 C16orf72 0.00375696 −0.255255837 1.07E−01 ENSG00000131507 NDFIP1 0.004173323 −0.242895723 6.80E−03 ENSG00000171310 CHST11 0.004536717 −0.14604981 1.20E−07 ENSG00000108510 MED13 0.005034555 −0.293870753 1.60E−03 ENSG00000162065 TBC1D24 0.005127762 −1.23071089 1 ENSG00000106609 TMEM248 0.005316307 −0.23621242 2.90E−07 ENSG00000131504 DIAPH1 0.005406879 −0.213577391 2.00E−04 ENSG00000110218 PANX1 0.005542647 −0.39874583 2.59E−02 ENSG00000123159 GIPC1 0.00645275 −0.478285755 6.90E−03 ENSG00000100105 PATZ1 0.00652701 −0.324460116 3.10E−03 ENSG00000153310 FAM49B 0.007506383 −0.139159484 2.00E−04 ENSG00000152601 MBNL1 0.00777836 −0.152181062 2.00E−11 ENSG00000151014 CCRN4L 0.007814184 −0.480208055 7.50E−03 ENSG00000168092 PAFAH1B2 0.008647229 −0.388340708 3.82E−02 ENSG00000119844 AFTPH 0.008725735 −0.591675727 1 ENSG00000139112 GABARAPL1 0.008844095 −1.233522978 1 ENSG00000066933 MYO9A 0.008868511 −0.473506657 1 ENSG00000120727 PAIP2 0.010801093 −0.157320231 5.59E−01 ENSG00000078369 GNB1 0.011642786 −0.133797709 5.00E−04 ENSG00000137845 ADAM10 0.012053048 −0.208903322 9.00E−10 ENSG00000169967 MAP3K2 0.013056576 −0.377048905 6.60E−03 ENSG00000177542 SLC25A22 0.013143394 −0.338628583 1.17E−01 ENSG00000106290 TAF6 0.014175182 −0.210235711 5.00E−04 ENSG00000105329 TGFB1 0.015301045 −0.221315351 2.00E−04 ENSG00000064490 RFXANK 0.015800837 −0.324746409 3.00E−04 ENSG00000180035 ZNF48 0.015918146 −0.582772982 1 ENSG00000160917 CPSF4 0.016200762 −0.319405125 1.70E−03 ENSG00000162889 MAPKAPK2 0.016286083 −0.352699883 5.49E−01 ENSG00000181027 FKRP 0.016390601 −0.996001717 1 ENSG00000065970 FOXJ2 0.017646559 −0.4735107 1 ENSG00000137822 TUBGCP4 0.017824276 −0.534568492 3.06E−02 ENSG00000109220 CHIC2 0.018242688 −0.521221308 1.70E−02 ENSG00000136878 USP20 0.019165529 −0.206602358 2.00E−08 ENSG00000163349 HIPK1 0.020020123 −0.282659771 2.00E−04 ENSG00000048405 ZNF800 0.020652909 −0.271097499 3.00E−08 ENSG00000145349 CAMK2D 0.021359574 −0.408237368 7.82E−02 ENSG00000100796 SMEK1 0.021404696 −0.176469607 1.00E−11 ENSG00000103502 CDIPT 0.021406946 −0.323954264 1.43E−01 ENSG00000124786 SLC35B3 0.023814954 −0.917840885 1 ENSG00000150995 ITPR1 0.025529346 −0.628260516 1 ENSG00000034677 RNF19A 0.025744017 −0.483894067 1 ENSG00000056998 GYG2 0.026501722 −0.929650779 1 ENSG00000204348 DOM3Z 0.026501738 −0.595853393 1 ENSG00000095380 NANS 0.027123309 −0.321819229 5.39E−02 ENSG00000130669 PAK4 0.02752902 −0.627975797 1 ENSG00000167978 SRRM2 0.027585188 −0.081656945 1.00E−04 ENSG00000112306 RPS12 0.029227861 −0.173199482 1.13E−01 ENSG00000172292 CERS6 0.029552171 −0.205124483 1.00E−09 ENSG00000102858 MGRN1 0.02977034 −0.309624822 1.40E−02 ENSG00000105063 PPP6R1 0.029786388 −0.157573098 1.00E−10 ENSG00000121083 DYNLL2 0.02989098 −0.137797441 1.00E−03

TABLE 4 rDiff positive genes have significant changes in ribosome footprint distribution Gene ID Gene Name rDiff (p-value) Translational Efficiency (p-value) log2(Translational Efficiency) ENSG00000002822 MAD1L1 1.70E−07 0.758278428 −0.03032717 ENSG00000003056 M6PR 8.05E−04 0.341786644 −0.06800052 ENSG00000004700 RECQL 1.00E−08 0.598214663 −0.04903859 ENSG00000004779 NDUFAB1 5.26E−06 0.902185935 0.006429888 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000006114 SYNRG 2.00E−09 0.411165702 0.079008553 ENSG00000008952 SEC62 9.90E−07 0.412197652 0.074389117 ENSG00000009307 CSDE1 5.60E−07 0.282559234 −0.043586952 ENSG00000009335 UBE3C 7.00E−08 0.96703173 0.005178317 ENSG00000009790 TRAF3IP3 2.00E−04 0.932693262 0.007653676 ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000010810 FYN 4.02E−04 0.194054982 −0.146493062 ENSG00000011295 TTC19 3.00E−04 0.726452954 0.048391976 ENSG00000011376 LARS2 6.02E−04 0.269847002 −0.142543886 ENSG00000013810 TACC3 2.00E−09 0.886452126 −0.009226853 ENSG00000018699 TTC27 3.00E−04 0.640010253 −0.057075791 ENSG00000021355 SERPINB1 4.00E−04 0.866004942 −0.014203345 ENSG00000021762 OSBPL5 7.01E−04 0.905417327 −0.030769757 ENSG00000027697 IFNGR1 4.00E−04 0.409322091 0.099560346 ENSG00000030066 NUP160 1.00E−11 0.645030987 −0.030045128 ENSG00000030419 IKZF2 3.00E−04 0.413365119 −0.055123312 ENSG00000031698 SARS 2.00E−04 0.872730663 0.011917 ENSG00000033030 ZCCHC8 6.10E−08 0.867990166 −0.021717099 ENSG00000033170 FUT8 6.00E−04 0.006226232 −0.355628717 ENSG00000033178 UBA6 4.00E−04 0.07871533 0.184240847 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000036257 CUL3 3.00E−04 0.568119382 0.048886832 ENSG00000038210 PI4K2B 1.01E−04 0.689067203 0.060060784 ENSG00000038219 BOD1L1 1.00E−04 0.003376816 0.278967432 ENSG00000038358 EDC4 3.00E−04 0.449660549 0.070646944 ENSG00000039123 SKIV2L2 5.00E−08 0.397584419 0.067295718 ENSG00000043462 LCP2 1.00E−04 0.236691265 −0.074243034 ENSG00000047315 POLR2B 9.04E−04 0.311086732 0.072452266 ENSG00000047410 TPR 2.00E−11 0.045762118 0.103472955 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000048740 CELF2 8.00E−04 0.039583811 0.136650125 ENSG00000049618 ARID1B 1.00E−04 0.385309666 0.127414641 ENSG00000051523 CYBA 1.00E−04 0.816434248 0.0204381 ENSG00000052841 TTC17 9.01E−04 0.972969728 0.004383509 ENSG00000054654 SYNE2 9.00E−09 0.143319349 −0.17547751 ENSG00000055044 NOP58 1.00E−11 0.905915474 −0.006508419 ENSG00000055130 CUL1 2.00E−04 0.24134893 −0.116033963 ENSG00000055163 CYFIP2 6.00E−13 0.757974081 −0.02427969 ENSG00000055483 USP36 2.00E−10 0.857880476 0.014047197 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000058668 ATP2B4 1.00E−09 0.000680955 −0.302809666 ENSG00000058729 RIOK2 1.00E−09 0.452540408 0.12495794 ENSG00000059573 ALDH18A1 4.00E−08 0.254939161 −0.109183666 ENSG00000060069 CTDP1 1.00E−04 0.606500761 −0.103959418 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000060339 CCAR1 1.00E−04 0.526971388 0.044049323 ENSG00000060491 OGFR 6.00E−04 0.881572577 −0.018437371 ENSG00000062650 WAPAL 8.00E−04 0.019004475 −0.211592796 ENSG00000062822 POLD1 1.00E−04 0.881523419 −0.010752676 ENSG00000063245 EPN1 6.00E−04 0.095672127 −0.260058118 ENSG00000064115 TM7SF3 3.00E−04 0.921247137 0.007233323 ENSG00000064419 TNPO3 1.00E−04 0.030219393 −0.182349237 ENSG00000064490 RFXANK 3.00E−04 0.015800837 −0.324746409 ENSG00000065150 IPO5 1.00E−04 0.241050243 0.063914843 ENSG00000065328 MCM10 3.00E−08 0.796034459 −0.019990672 ENSG00000065357 DGKA 7.00E−04 0.601907834 −0.04235016 ENSG00000065526 SPEN 1.00E−04 0.859973887 −0.020485515 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000066084 DIP2B 2.20E−08 0.728581353 0.041530278 ENSG00000066279 ASPM 2.00E−09 0.013635649 0.181712013 ENSG00000066654 THUMPD1 1.00E−04 0.066318449 0.218332022 ENSG00000067082 KLF6 6.00E−04 0.873448029 0.015089776 ENSG00000067167 TRAM1 1.80E−07 0.785985329 −0.016953438 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000067596 DHX8 2.00E−08 0.577229448 0.056415372 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000068796 KIF2A 1.00E−04 0.056041279 0.123499472 ENSG00000070756 PABPC1 1.00E−07 0.067231582 −0.133311245 ENSG00000071054 MAP4K4 3.00E−10 0.191479972 −0.114359829 ENSG00000071127 WDR1 1.00E−08 0.661342679 −0.016553317 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000071626 DAZAP1 5.20E−07 0.060128417 −0.110195121 ENSG00000071894 CPSF1 1.00E−04 0.292670446 −0.087303379 ENSG00000072062 PRKACA 5.00E−04 0.823686793 −0.022935317 ENSG00000072310 SREBF1 1.00E−04 0.744899078 −0.026352209 ENSG00000072364 AFF4 4.01E−04 0.18444246 −0.147821651 ENSG00000072778 ACADVL 2.01E−04 0.634381953 0.052306846 ENSG00000073060 SCARB1 4.00E−04 0.444106259 −0.124760329 ENSG00000073614 KDM5A 7.00E−04 0.292729244 −0.104574461 ENSG00000074370 ATP2A3 1.00E−04 0.51081004 −0.034487857 ENSG00000074603 DPP8 1.09E−06 0.371935225 −0.109929668 ENSG00000074695 LMAN1 6.00E−04 0.136972912 0.109603097 ENSG00000074755 ZZEF1 4.01E−04 0.145270305 0.179883886 ENSG00000075415 SLC25A3 3.30E−07 0.062332659 −0.064744845 ENSG00000075539 FRYL 1.00E−04 0.128443961 0.156722872 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000076108 BAZ2A 1.00E−04 0.708000473 −0.042895235 ENSG00000076770 MBNL3 2.60E−07 0.135662004 −0.159547551 ENSG00000077097 TOP2B 1.00E−04 0.84957972 0.01045839 ENSG00000077232 DNAJC10 2.00E−04 0.043053807 −0.322931196 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000078674 PCM1 5.00E−11 0.600752059 −0.058335335 ENSG00000078687 TNRC6C 3.00E−04 0.332794972 −0.148534844 ENSG00000079313 REXO1 7.00E−04 0.723402497 −0.050607046 ENSG00000079432 CIC 8.00E−04 0.820970963 −0.041443313 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000080345 RIF1 3.00E−11 0.722609171 0.022548991 ENSG00000080815 PSEN1 1.50E−07 0.468385762 −0.105188191 ENSG00000080986 NDC80 4.00E−04 0.202768868 0.097858575 ENSG00000081019 RSBN1 8.00E−04 0.864427786 −0.025477267 ENSG00000081237 PTPRC 7.00E−04 0.015733814 0.122576702 ENSG00000081791 KIAA0141 9.00E−04 0.905406058 −0.017374448 ENSG00000082212 ME2 8.00E−04 0.795777072 −0.028699073 ENSG00000082516 GEMIN5 1.00E−04 0.382720363 0.09923243 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −0.205302853 ENSG00000082898 XPO1 1.00E−11 0.026533538 −0.106116515 ENSG00000083312 TNPO1 8.00E−04 0.96323084 0.002633087 ENSG00000083642 PDS5B 6.00E−04 0.586150567 0.042212365 ENSG00000083845 RPS5 3.02E−04 0.290962665 −0.089607269 ENSG00000083857 FAT1 2.07E−09 0.602892898 −0.038812678 ENSG00000084093 REST 1.00E−09 0.221405653 −0.118069779 ENSG00000084207 GSTP1 8.00E−04 0.028975686 0.078499851 ENSG00000084733 RAB10 7.00E−08 0.078220422 −0.136343032 ENSG00000084774 CAD 2.00E−08 0.242515439 0.087577807 ENSG00000086102 NFX1 7.00E−04 0.176154723 0.162273705 ENSG00000086504 MRPL28 1.00E−04 0.056394 −0.151444666 ENSG00000086758 HUWE1 2.40E−11 0.464534104 −0.039863394 ENSG00000087087 SRRT 1.00E−10 0.966692349 0.001824104 ENSG00000087365 SF3B2 1.00E−04 0.108200543 0.071832895 ENSG00000087460 GNAS 3.00E−10 0.461136397 −0.032870857 ENSG00000088247 KHSRP 2.00E−04 0.673716802 −0.021332247 ENSG00000088325 TPX2 4.00E−13 0.000751758 −0.147886462 ENSG00000088930 XRN2 1.00E−04 0.054328641 0.120769979 ENSG00000089053 ANAPC5 2.00E−04 0.71210468 −0.020762022 ENSG00000089094 KDM2B 4.00E−08 0.242750733 −0.121485992 ENSG00000089154 GCN1L1 3.00E−09 0.913083626 −0.007259602 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000090061 CCNK 8.00E−08 0.870725186 −0.014115514 ENSG00000090372 STRN4 6.00E−04 0.942223216 0.00735298 ENSG00000090520 DNAJB11 1.00E−04 0.403800964 −0.067101447 ENSG00000090861 AARS 6.00E−04 0.574152586 0.035132718 ENSG00000091127 PUS7 9.00E−04 0.204909104 −0.155033013 ENSG00000091164 TXNL1 1.00E−07 0.371475872 −0.0727392 ENSG00000091317 CMTM6 2.00E−08 0.443439517 0.064753558 ENSG00000092094 OSGEP 2.00E−08 0.977762307 −0.002519015 ENSG00000092853 CLSPN 1.00E−10 0.062944195 0.125340878 ENSG00000092964 DPYSL2 1.72E−06 0.18869348 −0.144294954 ENSG00000093009 CDC45 4.00E−04 0.918341518 0.007977992 ENSG00000093167 LRRFIP2 1.00E−04 0.814819674 −0.032970227 ENSG00000095319 NUP188 5.00E−04 0.409660705 −0.062866839 ENSG00000096401 CDC5L 4.00E−11 0.958393737 −0.003388653 ENSG00000097046 CDC7 3.00E−04 0.543156786 −0.062966344 ENSG00000099331 MYO9B 6.00E−04 0.792985514 0.024635401 ENSG00000099381 SETD1A 1.00E−08 0.334979113 0.098318494 ENSG00000099991 CABIN1 1.00E−08 0.104911155 −0.208959207 ENSG00000100029 PES1 3.00E−04 0.805834098 −0.019606907 ENSG00000100138 NHP2L1 1.00E−04 0.451814068 −0.053140436 ENSG00000100147 CCDC134 6.00E−08 0.397335351 −0.115525081 ENSG00000100242 SUN2 4.00E−04 0.443353969 0.107423956 ENSG00000100258 LMF2 3.01E−04 0.446590324 −0.096455839 ENSG00000100280 AP1B1 1.00E−04 0.155202288 −0.113131916 ENSG00000100296 THOC5 1.00E−04 0.777068501 0.04404948 ENSG00000100345 MYH9 2.10E−13 0.195171025 −0.051020259 ENSG00000100350 FOXRED2 1.00E−04 0.939313293 −0.00792074 ENSG00000100401 RANGAP1 1.00E−04 0.59275986 −0.053239149 ENSG00000100403 ZC3H7B 4.00E−04 0.241293577 −0.127436934 ENSG00000100422 CERK 5.01E−04 0.767879843 −0.038668 ENSG00000100461 RBM23 2.00E−04 0.126115054 −0.188774943 ENSG00000100528 CNIH 2.00E−11 0.396062577 0.115843844 ENSG00000100554 ATP6V1D 1.00E−09 0.428461734 −0.082721884 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000100714 MTHFD1 5.00E−04 0.068239627 0.121426205 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −0.176469607 ENSG00000100813 ACIN1 1.00E−04 0.513552164 −0.041074263 ENSG00000100888 CHD8 5.00E−09 0.833778017 0.019607725 ENSG00000100911 PSME2 6.11E−04 0.954296798 −0.00949908 ENSG00000100994 PYGB 2.02E−04 0.741200463 0.05467102 ENSG00000100997 ABHD12 1.00E−08 0.489735178 −0.117139463 ENSG00000101161 PRPF6 5.00E−04 0.452014829 0.060790849 ENSG00000101182 PSMA7 5.01E−04 0.980181485 0.001199919 ENSG00000101191 DIDO1 9.00E−09 0.846657226 −0.024545447 ENSG00000101224 CDC25B 2.00E−09 0.25893922 0.059946483 ENSG00000101294 HM13 4.00E−04 0.788344267 −0.016820212 ENSG00000101310 SEC23B 2.00E−08 0.242275151 0.116563376 ENSG00000101343 CRNKL1 2.00E−04 0.587849423 0.05818265 ENSG00000101464 PIGU 7.02E−04 0.68308036 −0.052876011 ENSG00000101596 SMCHD1 1.00E−09 0.434566245 −0.059009881 ENSG00000101868 POLA1 2.00E−04 0.520751395 0.053293939 ENSG00000101972 STAG2 7.00E−04 0.001047325 −0.187270211 ENSG00000102054 RBBP7 1.60E−12 0.003411029 −0.129303881 ENSG00000102125 TAZ 7.01E−04 0.35021839 0.152681248 ENSG00000102189 EEA1 8.02E−04 0.70653248 −0.043342085 ENSG00000102245 CD40LG 1.00E−04 0.514830532 0.081808759 ENSG00000102606 ARHGEF7 6.00E−08 0.279523802 −0.128921833 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000102974 CTCF 1.00E−09 0.919312546 −0.009349348 ENSG00000103222 ABCC1 2.00E−04 0.969797812 0.002188323 ENSG00000103415 HMOX2 1.00E−09 0.569411146 0.05835055 ENSG00000103479 RBL2 1.00E−04 0.773913697 −0.038025558 ENSG00000103495 MAZ 1.30E−07 0.642227894 0.032737594 ENSG00000103544 C16orf62 3.01E−04 0.742406188 0.038231542 ENSG00000103591 AAGAB 9.00E−04 0.205123038 0.124804927 ENSG00000104177 MYEF2 7.01E−04 0.774370445 −0.035966517 ENSG00000104365 IKBKB 4.00E−04 0.474002406 0.087889302 ENSG00000104472 CHRAC1 8.00E−04 0.353904047 0.105337178 ENSG00000104517 UBR5 3.00E−10 0.744729033 0.031234126 ENSG00000104518 GSDMD 5.00E−04 0.437398468 −0.076674502 ENSG00000104549 SQLE 1.30E−07 0.043864022 −0.265964104 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000104738 MCM4 1.00E−10 0.915393017 0.003107424 ENSG00000104824 HNRNPL 3.60E−07 0.95648967 0.003621772 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000104852 SNRNP70 9.00E−04 0.594216034 −0.038334929 ENSG00000104886 PLEKHJ1 6.00E−08 0.445334658 0.068851577 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000105221 AKT2 2.00E−04 0.381664023 −0.141483695 ENSG00000105248 CCDC94 3.00E−04 0.324134308 −0.124113502 ENSG00000105281 SLC1A5 2.90E−10 0.106631749 −0.153858078 ENSG00000105329 TGFB1 2.00E−04 0.015301045 −0.221315351 ENSG00000105374 NKG7 9.00E−04 0.272175864 −0.097254231 ENSG00000105401 CDC37 2.02E−04 0.182664767 0.098508161 ENSG00000105486 LIG1 9.00E−04 0.865181674 −0.011170383 ENSG00000105618 PRPF31 4.00E−04 0.189221467 0.102321971 ENSG00000105676 ARMC6 8.00E−04 0.830466125 −0.018392253 ENSG00000105677 TMEM147 5.00E−08 0.824197085 −0.020622451 ENSG00000105810 CDK6 4.00E−08 4.76E−05 −0.145254993 ENSG00000105939 ZC3HAV1 4.00E−04 0.868091195 0.01093142 ENSG00000105953 OGDH 1.20E−08 0.404842964 −0.086222511 ENSG00000106263 EIF3B 1.00E−11 0.448608969 −0.028252846 ENSG00000106268 NUDT1 5.77E−06 0.36073421 0.053967036 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000106443 PHF14 6.00E−04 0.445863703 −0.062088645 ENSG00000106459 NRF1 1.01E−04 0.323046456 −0.119510858 ENSG00000106462 EZH2 3.20E−11 0.08121275 0.130806426 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000106624 AEBP1 1.10E−07 0.158176685 −0.063824438 ENSG00000106628 POLD2 1.00E−08 0.658612976 −0.035385479 ENSG00000106948 AKNA 1.00E−04 0.251174368 −0.100775455 ENSG00000107099 DOCK8 9.00E−10 0.488970714 −0.040530824 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000107223 EDF1 1.00E−09 0.174777133 0.108777319 ENSG00000107672 NSMCE4A 8.00E−04 0.421951683 −0.076069575 ENSG00000107854 TNKS2 1.00E−04 0.358901659 0.113182695 ENSG00000107937 GTPBP4 3.00E−04 0.193844537 0.095836593 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000108094 CUL2 4.00E−08 0.617398064 −0.046747644 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000108256 NUFIP2 5.00E−11 0.429062757 0.11100338 ENSG00000108270 AATF 1.00E−04 0.359806561 −0.064247245 ENSG00000108384 RAD51C 1.00E−09 0.010774857 0.189709393 ENSG00000108424 KPNB1 2.00E−11 8.66E−05 −0.171777065 ENSG00000108439 PNPO 3.00E−08 0.034630355 0.181670952 ENSG00000108479 GALK1 1.00E−04 0.608240213 −0.053110682 ENSG00000108506 INTS2 8.01E−04 0.295086648 0.109973837 ENSG00000108679 LGALS3BP 2.00E−08 0.973226652 0.000565498 ENSG00000108848 LUC7L3 2.60E−07 0.135191506 0.089311012 ENSG00000109062 SLC9A3R1 6.01E−04 0.122301958 −0.064055136 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000109332 UBE2D3 1.00E−08 0.601564183 0.04567695 ENSG00000109445 ZNF330 8.00E−04 0.392762523 −0.09281569 ENSG00000109606 DHX15 2.00E−04 0.687578939 0.016706661 ENSG00000109685 WHSC1 1.00E−11 0.0222009 −0.153361985 ENSG00000109805 NCAPG 9.00E−04 0.002277256 0.259598117 ENSG00000110047 EHD1 9.00E−04 0.373381573 −0.084500637 ENSG00000110075 PPP6R3 4.00E−08 0.652181808 −0.029536425 ENSG00000110108 TMEM109 1.00E−07 0.375160957 −0.055219962 ENSG00000110321 EIF4G2 2.00E−08 0.4789335 −0.030452093 ENSG00000110367 DDX6 6.00E−08 0.469603134 −0.047598358 ENSG00000110497 AMBRA1 5.02E−04 0.151399742 −0.200325064 ENSG00000110619 CARS 2.00E−04 0.186855283 0.157414334 ENSG00000110651 CD81 1.00E−04 0.010480682 −0.130640591 ENSG00000110713 NUP98 1.00E−10 0.656641011 −0.027832725 ENSG00000110955 ATP5B 4.00E−04 0.002969053 0.076326726 ENSG00000111335 OAS2 2.00E−04 0.677929702 0.048737643 ENSG00000111348 ARHGDIB 1.50E−07 0.037505737 −0.051698045 ENSG00000111602 TIMELESS 4.00E−04 0.702100642 0.024415465 ENSG00000111640 GAPDH 6.14E−04 0.68110279 0.024257691 ENSG00000111641 NOP2 1.00E−04 0.785381859 0.025711262 ENSG00000111642 CHD4 1.00E−04 0.289163376 0.048737019 ENSG00000111670 GNPTAB 5.01E−04 0.585766626 0.059976694 ENSG00000111726 CMAS 2.01E−04 0.649986681 0.073406219 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000111906 HDDC2 2.00E−04 0.810276479 −0.022306759 ENSG00000112029 FBXO5 2.00E−08 0.13434145 0.116650476 ENSG00000112159 MDN1 7.00E−08 0.503352158 0.068423753 ENSG00000112200 ZNF451 5.00E−04 0.487557618 0.072986258 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000112576 CCND3 2.00E−04 0.995647363 −0.00039872 ENSG00000112667 DNPH1 3.00E−08 0.220468437 0.223545108 ENSG00000112851 ERBB2IP 3.00E−04 0.005962767 −0.26900197 ENSG00000112972 HMGCS1 1.00E−10 0.049358853 0.122227347 ENSG00000112984 KIF20A 1.00E−08 0.934731349 −0.011172951 ENSG00000113369 ARRDC3 8.03E−04 0.778199879 0.045698203 ENSG00000113522 RAD50 4.00E−08 0.22034331 0.108849135 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000113649 TCERG1 5.00E−04 0.001091576 0.213551854 ENSG00000113810 SMC4 1.00E−11 0.586987805 −0.030468428 ENSG00000114023 FAM162A 1.00E−04 0.569698046 −0.05039296 ENSG00000114030 KPNA1 3.90E−07 0.001820335 −0.311253874 ENSG00000114126 TFDP2 7.00E−09 0.567162468 −0.026000796 ENSG00000114200 BCHE 6.02E−04 0.422143365 0.11979247 ENSG00000114416 FXR1 6.00E−04 0.827823905 0.018508158 ENSG00000114735 HEMK1 1.01E−04 0.020519619 −0.432698852 ENSG00000114737 CISH 2.01E−04 0.710188905 −0.018282662 ENSG00000114867 EIF4G1 4.00E−04 0.49755475 0.028286796 ENSG00000115020 PIKFYVE 7.00E−04 0.874274951 −0.045055571 ENSG00000115053 NCL 5.50E−07 0.060545427 0.042909924 ENSG00000115232 ITGA4 3.00E−09 0.73709161 −0.017356009 ENSG00000115306 SPTBN1 3.00E−14 0.008372115 −0.348514727 ENSG00000115419 GLS 4.00E−04 0.000197719 −0.269875671 ENSG00000115457 IGFBP2 3.00E−04 0.641399806 0.036552753 ENSG00000115464 USP34 1.00E−04 0.352056564 −0.122781815 ENSG00000115524 SF3B1 1.00E−04 0.157426391 0.074199855 ENSG00000115526 CHST10 6.00E−04 0.038600005 −0.351592853 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000115760 BIRC6 1.00E−04 0.297237048 0.088149326 ENSG00000115761 NOL10 9.00E−04 0.442727268 0.090675848 ENSG00000115806 GORASP2 4.00E−08 0.107877983 −0.140430182 ENSG00000115866 DARS 2.00E−08 0.047519868 −0.122885656 ENSG00000116120 FARSB 4.30E−07 0.448807369 0.078225185 ENSG00000116133 DHCR24 7.00E−04 0.242618057 −0.119340931 ENSG00000116213 WRAP73 5.00E−08 0.033620725 −0.365648037 ENSG00000116406 EDEM3 1.00E−04 0.160515088 0.161467793 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000116830 TTF2 1.00E−04 0.605327274 −0.05123716 ENSG00000116863 ADPRHL2 6.00E−04 0.363129878 0.185539492 ENSG00000116984 MTR 3.00E−04 0.692634133 −0.048662075 ENSG00000117318 ID3 4.00E−04 0.306098706 0.13190299 ENSG00000117523 PRRC2C 1.00E−11 0.24687917 0.051514482 ENSG00000117632 STMN1 4.01E−04 0.46870306 0.016853098 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000117724 CENPF 6.00E−04 0.178526649 0.061700857 ENSG00000117906 RCN2 3.00E−08 0.060079639 0.177995705 ENSG00000118007 STAG1 2.04E−04 0.802913841 −0.02813744 ENSG00000118058 MLL 3.50E−07 0.817626816 −0.021608686 ENSG00000118193 KIF14 2.00E−09 0.302902759 0.10403347 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000118513 MYB 2.00E−04 0.964892671 −0.004218901 ENSG00000118816 CCNI 6.90E−07 0.001528498 −0.189161037 ENSG00000119041 GTF3C3 1.00E−04 0.862861391 0.021723507 ENSG00000119397 CNTRL 5.00E−08 0.240770456 −0.130222735 ENSG00000119403 PHF19 2.01E−04 0.072821269 0.168059289 ENSG00000119596 YLPM1 4.00E−09 0.122997252 0.126832643 ENSG00000119638 NEK9 4.00E−04 0.69912267 −0.04034303 ENSG00000119669 IRF2BPL 3.02E−04 0.737023088 −0.046311272 ENSG00000119912 IDE 1.00E−04 0.846898243 −0.022139638 ENSG00000120071 KANSL1 5.00E−09 0.455238668 −0.080812302 ENSG00000120254 MTHFD1L 2.00E−04 0.953621846 0.005118686 ENSG00000120690 ELF1 1.00E−04 0.003793641 −0.220693753 ENSG00000120699 EXOSC8 6.00E−04 0.446432736 0.059033278 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000120738 EGR1 3.01E−04 0.317981925 −0.167567968 ENSG00000120800 UTP20 1.80E−07 0.730921404 0.032446721 ENSG00000120910 PPP3CC 7.00E−04 0.20233537 −0.200494687 ENSG00000121152 NCAPH 1.00E−04 0.569736027 0.064203664 ENSG00000121621 KIF18A 6.01E−04 0.278023728 −0.157166557 ENSG00000121691 CAT 5.00E−04 0.059201981 −0.151859968 ENSG00000121864 ZNF639 5.00E−04 0.468232115 −0.0841423 ENSG00000121892 PDS5A 2.00E−10 0.26251314 −0.063220359 ENSG00000122257 RBBP6 1.25E−09 0.000891329 −0.280964053 ENSG00000122862 SRGN 6.00E−04 0.307943894 −0.179460425 ENSG00000122882 ECD 1.00E−04 0.79331662 0.025252457 ENSG00000122966 CIT 9.00E−04 0.886264235 −0.011615594 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000123144 C19orf43 6.00E−04 0.121848164 0.139094396 ENSG00000123213 NLN 7.02E−04 0.499519365 0.090955024 ENSG00000123338 NCKAP1L 1.20E−11 0.299683199 0.062171215 ENSG00000123473 STIL 8.01E−04 0.246311874 −0.148306759 ENSG00000123485 HJURP 2.00E−08 0.006526616 0.216805783 ENSG00000123983 ACSL3 7.01E−04 0.236015207 0.104976406 ENSG00000124177 CHD6 7.01E−04 0.577660003 −0.071504202 ENSG00000124181 PLCG1 1.00E−04 0.95873485 −0.001417988 ENSG00000124193 SRSF6 3.00E−04 0.119574817 0.116472581 ENSG00000124228 DDX27 5.00E−08 0.834023162 0.015972497 ENSG00000124541 RRP36 2.00E−10 0.604769753 0.044529012 ENSG00000124575 HIST1H1D 1.00E−15 0.457298328 0.015260005 ENSG00000124641 MED20 1.00E−04 0.941332678 −0.01659058 ENSG00000124693 HIST1H3B 2.23E−12 0.254240878 0.040459312 ENSG00000124789 NUP153 3.20E−10 0.677271772 −0.045251116 ENSG00000125304 TM9SF2 7.00E−04 0.431186651 −0.044738316 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000125651 GTF2F1 1.10E−08 0.031215966 −0.168644284 ENSG00000125686 MED1 1.00E−08 0.18711587 −0.124662129 ENSG00000125755 SYMPK 1.00E−09 0.552114085 −0.054422769 ENSG00000125826 RBCK1 1.01E−04 0.817834713 −0.030877268 ENSG00000125885 MCM8 1.20E−07 0.740692289 −0.028115948 ENSG00000125971 DYNLRB1 2.10E−07 0.436287925 −0.07746413 ENSG00000126001 CEP250 7.10E−09 0.148680909 0.141831107 ENSG00000126804 ZBTB1 1.00E−04 0.453845337 −0.079720916 ENSG00000126883 NUP214 1.00E−04 0.847640341 −0.020473757 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000127184 COX7C 3.00E−04 0.392077126 −0.082208185 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −0.012039575 ENSG00000128191 DGCR8 2.00E−08 0.071123809 −0.242947421 ENSG00000128829 EIF2AK4 9.00E−04 0.627581021 −0.077669277 ENSG00000129317 PUS7L 2.00E−04 0.653028133 −0.054700064 ENSG00000129351 ILF3 1.30E−07 0.030039666 −0.082482869 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000130175 PRKCSH 3.00E−08 0.492538567 −0.034477239 ENSG00000130255 RPL36 1.40E−06 0.000331082 −0.237194765 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000130402 ACTN4 3.01E−04 0.05655675 −0.168897398 ENSG00000130640 TUBGCP2 2.00E−04 0.083088036 −0.263652098 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −0.092503983 ENSG00000130816 DNMT1 5.00E−04 0.595705453 −0.027738247 ENSG00000131148 EMC8 5.00E−11 0.89007858 −0.019540666 ENSG00000131174 COX7B 5.00E−04 0.280235251 −0.066677874 ENSG00000131446 MGAT1 5.01E−04 0.513530158 −0.076217655 ENSG00000131467 PSME3 3.01E−04 0.03715923 −0.116973165 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000132142 ACACA 1.00E−04 0.384701339 −0.088267863 ENSG00000132155 RAF1 1.90E−07 0.727868161 0.035824977 ENSG00000132182 NUP210 4.00E−11 0.396376427 −0.053178121 ENSG00000132294 EFR3A 6.00E−04 0.101176956 −0.138753026 ENSG00000132305 IMMT 2.00E−04 0.911802156 −0.008862008 ENSG00000132383 RPA1 1.00E−04 0.536237887 0.027348564 ENSG00000132436 FIGNL1 4.00E−04 0.90689028 0.012761853 ENSG00000132463 GRSF1 3.01E−04 0.003456732 0.144799456 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000132612 VPS4A 3.05E−06 0.187740524 −0.117542241 ENSG00000132646 PCNA 4.00E−09 0.449582299 0.020688405 ENSG00000132680 KIAA0907 7.00E−04 0.406235984 −0.089721055 ENSG00000132842 AP3B1 5.00E−04 0.894277559 0.020029663 ENSG00000132953 XPO4 4.00E−04 0.386914625 −0.098355739 ENSG00000133026 MYH10 1.00E−04 0.734506152 0.038657519 ENSG00000133454 MYO18B 6.00E−11 0.694394285 −0.024618977 ENSG00000133639 BTG1 7.00E−04 0.111632247 −0.307842825 ENSG00000133657 ATP13A3 1.00E−10 0.021301072 −0.237052311 ENSG00000133706 LARS 4.00E−04 0.597497941 −0.035619738 ENSG00000133961 NUMB 9.01E−04 0.646567716 0.059486807 ENSG00000134313 KIDINS220 1.00E−08 0.857549373 0.021963698 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000134480 CCNH 6.00E−04 0.669625945 0.058777209 ENSG00000134516 DOCK2 6.00E−04 0.505754891 0.037062588 ENSG00000134644 PUM1 2.00E−04 0.207254614 −0.119306565 ENSG00000134686 PHC2 8.90E−07 0.974560029 0.001948917 ENSG00000134697 GNL2 2.00E−08 0.31879467 0.080020877 ENSG00000134759 ELP2 2.00E−04 0.297463108 0.107815275 ENSG00000134910 STT3A 2.00E−11 0.248910784 0.068871835 ENSG00000134954 ETS1 5.70E−09 1.27E−05 −0.232324455 ENSG00000134987 WDR36 3.00E−04 0.028738034 0.151716239 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000135316 SYNCRIP 5.00E−08 0.141605449 −0.082838833 ENSG00000135439 AGAP2 6.00E−04 0.408030001 −0.104437193 ENSG00000135521 LTV1 9.00E−04 0.577086029 0.047229663 ENSG00000135679 MDM2 4.90E−07 0.948348125 0.012834459 ENSG00000135763 URB2 4.01E−04 0.668047421 0.04463194 ENSG00000135837 CEP350 1.00E−08 0.152171166 −0.140217831 ENSG00000135905 DOCK10 1.00E−08 0.717332641 0.040604232 ENSG00000135932 CAB39 1.00E−08 0.019948395 −0.200243436 ENSG00000135940 COX5B 4.00E−04 0.629646454 −0.025317297 ENSG00000136051 KIAA1033 2.00E−04 0.30132225 0.128371731 ENSG00000136068 FLNB 2.90E−12 0.062111584 −0.409977879 ENSG00000136104 RNASEH2B 4.20E−07 0.392137768 0.057232924 ENSG00000136146 MED4 8.00E−04 0.169595348 −0.110732537 ENSG00000136167 LCP1 2.00E−04 0.489381124 −0.018010751 ENSG00000136271 DDX56 1.10E−07 0.710493262 −0.028033209 ENSG00000136286 MYO1G 4.00E−08 0.20294865 0.071258537 ENSG00000136381 IREB2 3.00E−04 0.349257048 0.088289702 ENSG00000136492 BRIP1 3.00E−10 0.419920204 −0.069475773 ENSG00000136527 TRA2B 1.00E−04 0.403669503 −0.031939853 ENSG00000136536 MARCH7 1.00E−10 0.683034436 0.035756577 ENSG00000136628 EPRS 1.00E−04 0.75764814 0.018770161 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000136709 WDR33 9.00E−04 0.304508163 −0.081701638 ENSG00000136738 STAM 3.00E−04 0.366470963 0.094693082 ENSG00000136754 ABI1 2.00E−04 0.893753832 −0.015741049 ENSG00000136758 YME1L1 1.00E−04 0.090002669 −0.100978955 ENSG00000136824 SMC2 8.00E−04 0.373245909 0.054833376 ENSG00000136827 TOR1A 1.00E−08 0.306962116 0.113750173 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000136997 MYC 3.00E−08 0.000130485 −0.222358961 ENSG00000137076 TLN1 2.00E−09 0.114582751 −0.09941367 ENSG00000137106 GRHPR 3.00E−04 0.415762699 −0.09172823 ENSG00000137770 CTDSPL2 5.06E−04 0.972005432 −0.008284378 ENSG00000137776 SLTM 2.00E−04 0.100597307 0.119688243 ENSG00000137812 CASC5 9.01E−04 0.164406778 0.150771957 ENSG00000137818 RPLP1 3.04E−04 0.002330818 −0.514464579 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −0.208903322 ENSG00000138081 FBXO11 3.00E−04 0.421443356 −0.098168828 ENSG00000138095 LRPPRC 3.00E−04 0.234050395 −0.065104179 ENSG00000138107 ACTR1A 3.01E−04 0.37194789 −0.072733569 ENSG00000138182 KIF20B 1.00E−10 0.00406547 0.242659079 ENSG00000138231 DBR1 8.00E−04 0.870540124 0.016538189 ENSG00000138442 WDR12 6.00E−08 0.190351341 −0.142989262 ENSG00000138496 PARP9 1.00E−04 0.385276066 0.103537296 ENSG00000138592 USP8 7.06E−04 0.313673018 −0.181127726 ENSG00000138668 HNRNPD 2.40E−07 0.003261874 −0.098862205 ENSG00000138698 RAP1GDS1 5.00E−04 0.715002624 −0.035260421 ENSG00000138778 CENPE 2.00E−10 0.214004921 0.115990377 ENSG00000138795 LEF1 1.00E−09 1.60E−06 −0.210659864 ENSG00000138802 SEC24B 1.00E−09 0.515439824 −0.072741233 ENSG00000139154 AEBP2 2.00E−04 0.48380984 0.088405889 ENSG00000139197 PEX5 9.02E−04 0.510476835 0.078299498 ENSG00000139218 SCAF11 1.00E−08 0.50709776 −0.04074801 ENSG00000139350 NEDD1 1.00E−04 0.725169134 0.037847451 ENSG00000139505 MTMR6 4.00E−08 0.747037745 −0.038766186 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000139620 KANSL2 4.00E−04 0.2859956 0.116502184 ENSG00000139641 ESYT1 6.00E−04 0.115537694 0.094065695 ENSG00000139687 RB1 4.00E−11 0.227456544 0.062123731 ENSG00000139842 CUL4A 8.01E−04 0.735833147 −0.028312464 ENSG00000139946 PELI2 8.01E−04 0.84869402 −0.030488571 ENSG00000140259 MFAP1 4.00E−04 0.286171294 0.110298043 ENSG00000140262 TCF12 2.00E−10 0.025334533 −0.184064816 ENSG00000140299 BNIP2 9.00E−08 0.453644947 0.060595449 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000140525 FANCI 2.00E−04 0.688024573 0.029180218 ENSG00000140829 DHX38 8.00E−08 0.404193545 −0.083781852 ENSG00000140943 MBTPS1 4.00E−04 0.905572549 0.017038735 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000141252 VPS53 2.00E−04 0.91838956 0.011174255 ENSG00000141367 CLTC 2.00E−15 0.808942699 −0.009782716 ENSG00000141378 PTRH2 1.00E−04 0.917590739 −0.014270194 ENSG00000141456 PELP1 2.00E−04 0.806300676 0.019902797 ENSG00000141551 CSNK1D 5.00E−04 0.119201328 −0.129522549 ENSG00000141556 TBCD 1.00E−04 0.591494459 −0.026526545 ENSG00000142002 DPP9 1.00E−04 0.734190324 −0.049637386 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000143106 PSMA5 4.00E−08 0.382567623 0.045346574 ENSG00000143401 ANP32E 1.00E−04 0.915890957 0.004516508 ENSG00000143442 POGZ 2.00E−09 0.037681202 −0.207363006 ENSG00000143476 DTL 3.01E−04 0.748549723 −0.021380096 ENSG00000143514 TP53BP2 7.00E−04 0.283581835 −0.117348193 ENSG00000143624 INTS3 7.01E−04 0.265735445 −0.146742464 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000143924 EML4 7.01E−04 0.028666301 −0.26184158 ENSG00000144028 SNRNP200 8.00E−14 0.023390105 0.101854033 ENSG00000144554 FANCD2 2.00E−04 0.730926111 0.036291397 ENSG00000144559 TAMM41 5.00E−04 0.851527782 0.02836682 ENSG00000144580 RQCD1 2.00E−08 0.506022372 −0.045037202 ENSG00000144895 EIF2A 9.00E−04 0.746023779 −0.024414611 ENSG00000145041 VPRBP 4.00E−04 0.348933992 −0.094987498 ENSG00000145375 SPATA5 1.00E−04 0.784103808 −0.049246739 ENSG00000145604 SKP2 1.00E−04 0.979279396 0.003747348 ENSG00000145675 PIK3R1 4.02E−04 0.168588299 −0.102576778 ENSG00000145741 BTF3 5.00E−04 0.339388798 −0.072822964 ENSG00000145833 DDX46 2.00E−04 0.23392151 0.072701228 ENSG00000146457 WTAP 3.00E−04 0.883760976 0.015398065 ENSG00000146918 NCAPG2 1.50E−07 0.276197103 0.072778556 ENSG00000147130 ZMYM3 2.00E−04 0.059490308 −0.195960662 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000147677 EIF3H 4.01E−04 0.507259945 −0.031197371 ENSG00000148175 STOM 5.00E−04 0.202025121 −0.203176311 ENSG00000148229 POLE3 6.06E−04 0.60752674 −0.042630647 ENSG00000148334 PTGES2 1.04E−04 0.626929001 −0.068481398 ENSG00000148337 CIZ1 3.00E−04 0.65773939 −0.053627564 ENSG00000148396 SEC16A 1.00E−04 0.806810949 0.025438251 ENSG00000148400 NOTCH1 1.00E−04 0.276344103 −0.101708517 ENSG00000148773 MKI67 1.00E−10 0.123777629 0.063404366 ENSG00000148840 PPRC1 5.00E−04 0.85534363 −0.028695475 ENSG00000148843 PDCD11 5.00E−04 0.56753983 −0.05144919 ENSG00000149262 INTS4 4.00E−04 0.697964901 0.097540919 ENSG00000149273 RPS3 2.35E−05 0.448604972 −0.041417003 ENSG00000149308 NPAT 2.00E−04 0.81995279 0.029267153 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000149554 CHEK1 3.00E−08 0.029907425 0.142987957 ENSG00000149806 FAU 3.02E−04 0.009610398 0.1703503 ENSG00000149925 ALDOA 3.02E−04 0.183371478 −0.061277735 ENSG00000150990 DHX37 2.00E−04 0.614661587 −0.044689634 ENSG00000151131 C12orf45 8.00E−04 0.485034329 −0.088403349 ENSG00000151366 NDUFC2 2.00E−09 0.361312276 −0.043896664 ENSG00000151502 VPS26B 2.00E−04 0.277634848 0.100319458 ENSG00000151503 NCAPD3 3.00E−04 0.100416068 0.106975594 ENSG00000151694 ADAM17 7.30E−07 0.446223538 −0.1096626 ENSG00000151702 FLI1 1.00E−04 0.221034285 −0.138078723 ENSG00000151835 SACS 2.00E−04 0.575717819 0.054319675 ENSG00000152082 MZT2B 1.30E−08 0.784207016 −0.02186646 ENSG00000152147 GEMIN6 8.00E−04 0.112633984 0.186427654 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −0.152181062 ENSG00000152818 UTRN 1.00E−04 0.61246869 −0.063349119 ENSG00000153187 HNRNPU 3.00E−04 0.973831029 −0.000601876 ENSG00000153283 CD96 2.00E−04 0.267330877 −0.089143298 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000153922 CHD1 3.00E−09 0.997926928 −0.000811209 ENSG00000154370 TRIM11 3.01E−04 0.010190424 −0.431525912 ENSG00000155097 ATP6V1C1 4.00E−04 0.714750549 −0.035031119 ENSG00000155561 NUP205 1.00E−10 0.810978988 −0.015620768 ENSG00000155827 RNF20 1.00E−08 0.674024322 0.06246891 ENSG00000156273 BACH1 6.00E−04 0.916576258 −0.031050024 ENSG00000156858 PRR14 1.10E−07 0.581714014 −0.069166264 ENSG00000156875 HIAT1 1.00E−04 0.380713082 −0.10910263 ENSG00000156970 BUB1B 4.00E−10 0.947953681 0.006781777 ENSG00000156983 BRPF1 4.00E−04 0.933570558 −0.010817335 ENSG00000157540 DYRK1A 2.00E−09 0.276566574 −0.107710063 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000158290 CUL4B 1.00E−04 0.931575328 −0.009597839 ENSG00000158373 HIST1H2BD 2.00E−08 0.665459706 −0.010325486 ENSG00000158406 HIST1H4H 5.50E−09 0.616647851 0.034929668 ENSG00000158526 TSR2 1.00E−04 0.033164157 0.270897208 ENSG00000158623 COPG2 2.00E−04 0.583240481 −0.080548482 ENSG00000158864 NDUFS2 1.40E−07 0.692802138 0.037508569 ENSG00000158985 CDC42SE2 8.00E−08 0.027991366 −0.145160094 ENSG00000159131 GART 7.00E−04 0.231639477 −0.068059954 ENSG00000159140 SON 1.20E−12 0.122942939 0.067823184 ENSG00000159314 ARHGAP27 2.00E−04 0.839973686 −0.028088528 ENSG00000159720 ATP6V0D1 5.00E−04 0.616798782 0.050867945 ENSG00000160294 MCM3AP 2.00E−04 0.271306147 −0.134887854 ENSG00000160710 ADAR 2.00E−04 0.080829161 −0.088103689 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000160949 TONSL 1.00E−04 0.196335035 −0.17410121 ENSG00000161618 ALDH16A1 2.02E−04 0.73604894 −0.075930576 ENSG00000161980 POLR3K 3.00E−04 0.780264569 0.030710578 ENSG00000162434 JAK1 3.00E−04 0.381361282 −0.087910305 ENSG00000162607 USP1 5.00E−11 0.111472525 −0.094654587 ENSG00000162642 C1orf52 7.06E−04 0.242610098 0.178613459 ENSG00000162664 ZNF326 9.00E−04 0.113292053 0.1523951 ENSG00000163104 SMARCAD1 1.00E−07 0.928265836 −0.008266525 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000163607 GTPBP8 1.00E−04 0.426296869 −0.158064045 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000163808 KIF15 1.00E−04 0.593535319 0.070077932 ENSG00000163902 RPN1 3.00E−04 0.036709758 0.092942803 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000163939 PBRM1 2.00E−04 0.686874801 −0.037496 ENSG00000163946 FAM208A 1.00E−08 0.438939056 −0.067851035 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000164168 TMEM184C 2.50E−08 0.015050183 −0.397412646 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000164209 SLC25A46 2.00E−04 0.530752611 0.054652482 ENSG00000164754 RAD21 1.00E−08 0.756335554 −0.013371036 ENSG00000164978 NUDT2 1.01E−04 0.680662594 −0.053435289 ENSG00000164985 PSIP1 1.00E−04 0.469682012 0.047128687 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000165271 NOL6 2.00E−08 0.335093224 −0.094631942 ENSG00000165304 MELK 2.00E−04 0.351342781 0.077213211 ENSG00000165417 GTF2A1 7.00E−11 0.844760071 −0.015019218 ENSG00000165480 SKA3 2.00E−04 0.96112422 0.004310634 ENSG00000165494 PCF11 2.00E−09 0.168402482 −0.149826279 ENSG00000165502 RPL36AL 5.00E−08 0.586754886 −0.050125431 ENSG00000165527 ARF6 1.00E−10 0.156807609 −0.122434848 ENSG00000165678 GHITM 2.00E−09 0.40434721 −0.044927385 ENSG00000165782 TMEM55B 1.00E−04 0.742872155 0.097568043 ENSG00000165916 PSMC3 2.00E−04 0.327136153 0.067066757 ENSG00000166037 CEP57 1.00E−04 0.563570438 −0.056277887 ENSG00000166226 CCT2 2.00E−04 0.424973179 0.028289737 ENSG00000166747 AP1G1 1.00E−04 0.033859721 −0.180376252 ENSG00000166888 STAT6 1.00E−04 0.047894287 −0.21884119 ENSG00000166963 MAP1A 1.00E−09 0.569547165 0.03924313 ENSG00000166986 MARS 9.00E−08 0.040009981 −0.120193487 ENSG00000167258 CDK12 5.00E−04 0.030045657 −0.185190158 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000167468 GPX4 7.00E−04 0.056273288 0.118694036 ENSG00000167470 MIDN 3.00E−04 0.037975203 −0.404562969 ENSG00000167491 GATAD2A 3.00E−04 0.460886475 −0.052425426 ENSG00000167522 ANKRD11 1.00E−08 0.255387498 0.10026816 ENSG00000167548 MLL2 7.70E−09 0.196266437 −0.106714093 ENSG00000167658 EEF2 8.00E−09 0.147519118 −0.034288496 ENSG00000167670 CHAF1A 1.00E−08 0.388610811 −0.064999638 ENSG00000167747 C19orf48 1.80E−07 0.222151707 −0.136113219 ENSG00000167775 CD320 6.01E−04 0.822695325 0.022736769 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000168159 RNF187 5.00E−04 0.806336099 0.019371782 ENSG00000168264 IRF2BP2 7.60E−07 0.400567441 −0.098542726 ENSG00000168298 HIST1H1E 8.00E−12 0.575494886 0.00693283 ENSG00000168374 ARF4 2.00E−04 0.706405122 −0.070945614 ENSG00000168476 REEP4 8.00E−04 0.228797357 −0.127937767 ENSG00000168575 SLC20A2 4.02E−04 0.354909308 −0.119617959 ENSG00000168906 MAT2A 3.00E−04 0.308184492 −0.065364304 ENSG00000168918 INPP5D 3.00E−04 0.934564983 0.00569134 ENSG00000169018 FEM1B 3.00E−04 0.01910054 −0.397020738 ENSG00000169221 TBC1D10B 8.00E−04 0.845261963 0.037666933 ENSG00000169251 NMD3 3.03E−04 0.950093056 −0.00374493 ENSG00000169375 SIN3A 3.00E−04 0.134711475 −0.125528448 ENSG00000169710 FASN 1.10E−11 0.30709726 −0.046236104 ENSG00000169813 HNRNPF 2.00E−04 0.261636371 −0.045390453 ENSG00000169905 TOR1AIP2 7.00E−04 0.025144824 −0.223803399 ENSG00000169994 MYO7B 3.30E−14 0.067830781 −0.06063889 ENSG00000170004 CHD3 1.00E−08 0.982259628 0.001839786 ENSG00000170242 USP47 2.00E−09 0.545269342 −0.072546866 ENSG00000170430 MGMT 4.00E−04 0.64248843 0.054326376 ENSG00000171202 TMEM126A 8.07E−04 0.731670543 0.060950022 ENSG00000171298 GAA 1.10E−08 0.092998845 −0.248293341 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000171608 PIK3CD 2.00E−08 0.621359547 −0.054808961 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −0.150308959 ENSG00000171861 RNMTL1 8.04E−04 0.07761122 0.249083661 ENSG00000172046 USP19 5.00E−04 0.245610178 −0.156637412 ENSG00000172053 QARS 5.00E−04 0.867300993 0.013028643 ENSG00000172292 CERS6 1.00E−09 0.029552171 −0.205124483 ENSG00000172534 HCFC1 2.87E−12 6.58E−09 −0.313512877 ENSG00000172590 MRPL52 2.10E−06 0.325139446 −0.06780364 ENSG00000172716 SLFN11 2.00E−04 0.664664806 0.04271628 ENSG00000172725 CORO1B 6.00E−04 0.292853887 −0.118190498 ENSG00000172775 FAM192A 1.00E−04 0.366617379 −0.209977577 ENSG00000172795 DCP2 4.00E−04 0.294839777 0.094471533 ENSG00000172893 DHCR7 8.00E−08 0.073439676 −0.22022124 ENSG00000172939 OXSR1 2.01E−04 0.260117099 −0.092965672 ENSG00000172995 ARPP21 7.01E−04 0.648766475 −0.073812799 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000173141 MRP63 1.00E−11 0.385791511 0.081117583 ENSG00000173163 COMMD1 7.00E−04 0.313197556 0.20935172 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000173585 CCR9 4.00E−04 0.004934791 −0.343972085 ENSG00000173598 NUDT4 4.01E−04 0.997345883 −0.001074841 ENSG00000173674 EIF1AX 8.00E−04 0.780846703 0.072635112 ENSG00000173692 PSMD1 2.00E−09 0.749735343 0.022709414 ENSG00000173821 RNF213 1.00E−10 0.78788961 0.011822428 ENSG00000174010 KLHL15 8.01E−04 0.770357983 −0.039693382 ENSG00000174173 TRMT10C 2.00E−04 0.047069196 0.19484858 ENSG00000174197 MGA 2.30E−08 0.926221975 0.009158715 ENSG00000174231 PRPF8 1.00E−10 0.595739886 0.019539188 ENSG00000174238 PITPNA 3.00E−04 0.470422902 −0.066848619 ENSG00000174579 MSL2 5.00E−04 0.027763257 −0.205275001 ENSG00000174851 YIF1A 4.00E−04 0.662843111 0.058226495 ENSG00000175216 CKAP5 1.50E−08 0.03814885 0.117491174 ENSG00000175221 MED16 3.82E−06 0.907545434 −0.022207491 ENSG00000175467 SART1 1.00E−04 0.126941788 −0.10443742 ENSG00000175931 UBE2O 3.00E−04 0.447757287 0.068133312 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000176890 TYMS 4.00E−04 0.016419414 0.072462812 ENSG00000177084 POLE 1.00E−11 0.256661974 0.078668239 ENSG00000177156 TALDO1 8.00E−04 0.975031972 −0.001808282 ENSG00000177370 TIMM22 9.00E−04 0.455177571 0.122153476 ENSG00000177731 FLII 2.00E−04 0.139734019 0.11682969 ENSG00000177733 HNRNPA0 2.00E−04 0.789027425 0.010338975 ENSG00000177885 GRB2 1.00E−08 0.474905024 −0.037372741 ENSG00000178202 KDELC2 5.00E−04 0.480571508 0.092686527 ENSG00000178252 WDR6 1.00E−04 0.9305271 0.005862339 ENSG00000178921 PFAS 5.00E−04 0.196160647 0.110574411 ENSG00000179085 DPM3 4.00E−04 0.434227322 0.195823923 ENSG00000179091 CYC1 6.02E−04 0.55486733 0.052028776 ENSG00000179262 RAD23A 5.10E−07 0.674786887 0.038029829 ENSG00000179409 GEMIN4 7.20E−07 0.143223537 −0.152149612 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 ENSG00000180573 HIST1H2AC 7.04E−04 0.896293947 −0.002455334 ENSG00000181090 EHMT1 9.00E−04 0.697892305 0.047799788 ENSG00000181192 DHTKD1 5.06E−04 0.791904623 −0.080578455 ENSG00000181222 POLR2A 1.00E−12 0.038830003 −0.102840994 ENSG00000181555 SETD2 3.00E−04 0.918631253 0.007282024 ENSG00000181789 COPG1 3.00E−04 0.241621066 0.077715176 ENSG00000182473 EXOC7 6.00E−04 0.343587671 −0.074730044 ENSG00000182481 KPNA2 3.00E−04 0.644150482 −0.032122311 ENSG00000182551 ADI1 9.00E−04 0.372377154 0.072506123 ENSG00000182827 ACBD3 3.00E−08 0.404828614 0.130448872 ENSG00000183495 EP400 6.00E−04 0.637303595 0.055214724 ENSG00000183918 SH2D1A 7.01E−04 0.283846866 0.067991179 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000184357 HIST1H1B 3.00E−14 0.101743718 0.056835835 ENSG00000184432 COPB2 1.00E−04 0.99225242 0.000643147 ENSG00000184445 KNTC1 3.00E−04 0.290700324 0.117936173 ENSG00000184634 MED12 2.00E−09 0.441484568 0.08225596 ENSG00000184661 CDCA2 6.00E−04 0.129977922 −0.116602274 ENSG00000184719 RNLS 9.00E−04 0.124096231 −0.160207128 ENSG00000184825 HIST1H2AH 1.50E−08 0.236178337 0.035788181 ENSG00000184990 SIVA1 5.01E−04 0.001360314 0.174493974 ENSG00000185000 DGAT1 3.01E−04 0.711930638 −0.055676496 ENSG00000185104 FAF1 1.00E−04 0.186505473 −0.111825327 ENSG00000185163 DDX51 4.22E−06 0.69311416 −0.05606435 ENSG00000185236 RAB11B 9.00E−04 0.250648111 −0.08681802 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000185344 ATP6V0A2 2.03E−04 0.449082903 0.078626222 ENSG00000186106 ANKRD46 1.00E−08 0.938464567 0.008636835 ENSG00000186298 PPP1CC 9.02E−04 0.246006029 −0.058739406 ENSG00000186395 KRT10 1.00E−04 0.616095519 0.04261803 ENSG00000186480 INSIG1 3.08E−06 0.573173068 −0.037858571 ENSG00000186517 ARHGAP30 1.00E−04 0.332792401 0.068602551 ENSG00000186566 GPATCH8 9.00E−04 0.836769737 −0.022374401 ENSG00000186575 NF2 5.00E−04 0.511808 0.06843328 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000187257 RSBN1L 2.10E−07 0.682200483 0.045962809 ENSG00000187531 SIRT7 4.01E−04 0.591150723 −0.160016903 ENSG00000187764 SEMA4D 4.00E−04 0.413891066 −0.073148377 ENSG00000187837 HIST1H1C 3.00E−09 0.000257571 0.053651622 ENSG00000188229 TUBB4B 6.00E−08 0.176644347 0.091849122 ENSG00000188486 H2AFX 2.64E−06 0.075491176 0.09777223 ENSG00000188987 HIST1H4D 1.00E−13 0.875362395 0.003774928 ENSG00000196155 PLEKHG4 1.00E−04 0.015595222 −0.295432913 ENSG00000196230 TUBB 2.40E−07 0.534866787 0.035871882 ENSG00000196235 SUPT5H 2.00E−04 0.195564051 −0.152021425 ENSG00000196305 IARS 3.00E−04 0.401865475 0.075934866 ENSG00000196367 TRRAP 3.00E−10 0.181318964 −0.088383498 ENSG00000196396 PTPN1 2.00E−04 0.634603291 0.040420571 ENSG00000196498 NCOR2 6.00E−04 0.072769487 −0.155938346 ENSG00000196504 PRPF40A 1.00E−09 0.142009995 0.08561315 ENSG00000196535 MYO18A 6.00E−04 0.972106963 −0.002927619 ENSG00000196683 TOMM7 3.00E−08 0.90908379 −0.015495382 ENSG00000196700 ZNF512B 2.09E−04 0.699101376 0.063580592 ENSG00000196787 HIST1H2AG 5.50E−08 0.747550904 −0.019583582 ENSG00000196924 FLNA 1.00E−12 0.169192017 −0.078099713 ENSG00000197061 HIST1H4C 1.00E−09 0.897532466 0.002378482 ENSG00000197081 IGF2R 4.10E−09 0.531193218 0.066454289 ENSG00000197102 DYNC1H1 5.00E−10 0.149889643 0.128641432 ENSG00000197153 HIST1H3J 7.00E−11 0.888297027 −0.007272098 ENSG00000197157 SND1 1.01E−04 0.257912014 0.060457678 ENSG00000197312 DDI2 6.01E−04 0.856181146 −0.025215686 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000197409 HIST1H3D 3.00E−12 0.512483364 −0.019287888 ENSG00000197601 FAR1 3.30E−08 0.659187685 −0.041267074 ENSG00000197694 SPTAN1 2.00E−10 0.081327953 −0.18679623 ENSG00000197697 HIST1H2BE 9.00E−08 0.493425798 0.028198489 ENSG00000197746 PSAP 2.00E−10 0.088797396 0.046479701 ENSG00000197903 HIST1H2BK 2.00E−04 0.781823807 −0.022923109 ENSG00000197930 ERO1L 6.50E−07 0.973303548 −0.003430597 ENSG00000198015 MRPL42 2.00E−04 0.883226659 −0.031389992 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000198231 DDX42 6.00E−11 0.824728919 −0.015904689 ENSG00000198276 UCKL1 3.30E−07 0.304042297 −0.145350623 ENSG00000198327 HIST1H4F 3.00E−09 0.208678387 −0.022044471 ENSG00000198339 HIST1H4I 2.00E−08 0.495872312 0.011398728 ENSG00000198374 HIST1H2AL 2.05E−06 0.072591854 0.039969658 ENSG00000198380 GFPT1 2.00E−04 0.636068909 0.045606566 ENSG00000198520 C1orf228 7.80E−07 0.473771444 −0.055437679 ENSG00000198563 DDX39B 8.00E−04 0.271266603 −0.112598519 ENSG00000198604 BAZ1A 5.00E−10 0.704916782 −0.030835374 ENSG00000198646 NCOA6 4.01E−04 0.116549501 −0.173636683 ENSG00000198648 STK39 5.01E−04 0.740902509 0.034721562 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000198730 CTR9 1.00E−09 0.11470634 −0.142355213 ENSG00000198786 MT-ND5 2.00E−08 0.038698438 −0.086785336 ENSG00000198824 CHAMP1 4.00E−04 0.249023725 −0.097569413 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000198917 C9orf114 8.03E−04 0.004093641 0.394051515 ENSG00000198952 SMG5 3.00E−04 0.489633279 0.073022366 ENSG00000203813 HIST1H3H 1.00E−04 0.178969463 −0.025149763 ENSG00000204138 PHACTR4 6.00E−08 0.121133788 −0.222449915 ENSG00000204178 TMEM57 3.00E−04 0.010544799 −0.345157048 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000204256 BRD2 1.00E−08 0.232280315 −0.080114261 ENSG00000204371 EHMT2 1.00E−08 0.297240081 0.090410757 ENSG00000204394 VARS 5.00E−04 0.304208452 −0.069883333 ENSG00000204469 PRRC2A 2.00E−09 0.549464658 0.030387491 ENSG00000204713 TRIM27 8.00E−04 0.790207031 −0.026814299 ENSG00000205268 PDE7A 3.00E−04 0.558620633 −0.048541326 ENSG00000205336 GPR56 8.01E−04 0.228558377 −0.136323001 ENSG00000205629 LCMT1 1.00E−04 0.552673909 −0.089560402 ENSG00000205744 DENND1C 8.04E−04 0.849269508 −0.026567467 ENSG00000213064 SFT2D2 8.00E−04 0.081132453 −0.203416362 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000215301 DDX3X 2.00E−04 0.924710307 −0.00796857 ENSG00000216490 IFI30 4.13E−04 0.518872644 −0.117960608 ENSG00000221829 FANCG 1.00E−04 0.38011695 0.102243151 ENSG00000227057 WDR46 1.00E−10 0.24341875 0.098260531 ENSG00000231925 TAPBP 2.00E−04 0.970644204 −0.003684474 ENSG00000233224 HIST1H2AM 1.00E−11 0.547023548 −0.003832791 ENSG00000234127 TRIM26 9.02E−04 0.038240212 −0.218304118 ENSG00000241978 AKAP2 1.00E−08 0.863267602 0.030178646 ENSG00000253729 PRKDC 1.00E−12 0.427584653 0.050339925 ENSG00000254870 ATP6V1G2-DDX39B 7.01E−04 0.57599435 0.036177813 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000261661 RP11-31I10.4 1.27E−13 NaN NaN ENSG00000267740 AC024592.12 4.00E−04 0.536893222 −0.044671372

TABLE 5 Genes that are both TE down and rDiff positive Gene ID Gene Name Translational Efficiency (p-value) log2(Translational Efficiency) rDiff (p-value) ENSG00000137845.9 ADAM10 0.012053048 −0.208903322 8.99999E−10 ENSG00000133657.10 ATP13A3 0.021301072 −0.237052311 9.99999E−11 ENSG00000058668.10 ATP2B4 0.000680955 −0.302809666 9.9999E−10 ENSG00000127152.13 BCL11B 5.40428E−10 −0.517770746  9.999E−09 ENSG00000135932.6 CAB39 0.019948395 −0.200243436  9.999E−09 ENSG00000118816.5 CCNI 0.001528498 −0.189161037 6.89931E−07 ENSG00000173585.11 CCR9 0.004934791 −0.343972085 0.00040005 ENSG00000110651.6 CD81 0.010480682 −0.130640591 0.00010002 ENSG00000158985.9 CDC42SE2 0.027991366 −0.145160094  7.9992E−08 ENSG00000105810.5 CDK6 4.75568E−05 −0.145254993  3.9996E−08 ENSG00000172292.10 CERS6 0.029552171 −0.205124483  9.9999E−10 ENSG00000171310.6 CHST11 0.004536717 −0.14604981 1.19988E−07 ENSG00000131504.11 DIAPH1 0.005406879 −0.213577391 0.0002 ENSG00000120690.9 ELF1 0.003793641 −0.220693753 0.0001 ENSG00000143924.14 EML4 0.028666301 −0.26184158 0.00070056 ENSG00000112851.10 ERBB2IP 0.005962767 −0.26900197 0.00030017 ENSG00000134954.9 ETS1 1.26966E−05 −0.232324455 5.69999E−09 ENSG00000153310.13 FAM49B 0.007506383 −0.139159484 0.0002 ENSG00000169018.5 FEM1B 0.01910054 −0.397020738 0.00030007 ENSG00000033170.12 FUT8 0.006226232 −0.355628717 0.00060004 ENSG00000115419.8 GLS 0.000197719 −0.269875671 0.00040019 ENSG00000078369.10 GNB1 0.011642786 −0.133797709 0.00050004 ENSG00000172534.9 HCFC1 6.57909E−09 −0.313512877   2.87E−12 ENSG00000114735.5 HEMK1 0.020519619 −0.432698852 0.00010083 ENSG00000163349.15 HIPK1 0.020020123 −0.282659771 0.00020003 ENSG00000138668.14 HNRNPD 0.003261874 −0.098862205 2.39976E−07 ENSG00000114030.8 KPNA1 0.001820335 −0.311253874 3.89961E−07 ENSG00000108424.5 KPNB1 8.66259E−05 −0.171777065 2E−11 ENSG00000138795.5 LEF1 1.59715E−06 −0.210659864  9.9999E−10 ENSG00000152601.13 MBNL1 0.00777836 −0.152181062 2E−11 ENSG00000123066.3 MED13L 4.78765E−05 −0.415941737 2.19998E−08 ENSG00000174579.3 MSL2 0.027763257 −0.205275001 0.0005 ENSG00000149480.2 MTA2 2.63948E−05 −0.22354576 5.99994E−09 ENSG00000136997.10 MYC 0.000130485 −0.222358961  2.9997E−08 ENSG00000196155.8 PLEKHG4 0.015595222 −0.295432913 0.00010019 ENSG00000105063.14 PPP6R1 0.029786388 −0.157573098 9.99999E−11 ENSG00000171522.5 PTGER4 0.002288634 −0.274827847 2.39976E−07 ENSG00000184007.11 PTP4A2 0.00039459 −0.142942918 1.49985E−07 ENSG00000122257.14 RBBP6 0.000891329 −0.280964053   1.25E−09 ENSG00000102054.12 RBBP7 0.003411029 −0.129303881   1.6E−12 ENSG00000064490.7 RFXANK 0.015800837 −0.324746409 0.00030015 ENSG00000130255.8 RPL36 0.000331082 −0.237194765 1.39986E−06 ENSG00000137818.7 RPLP1 0.002330818 −0.514464579 0.00030353 ENSG00000100796.13 SMEK1 0.021404696 −0.176469607     1E−11 ENSG00000115306.10 SPTBN1 0.008372115 −0.348514727     3E−14 ENSG00000167978.11 SRRM2 0.027585188 −0.081656945 0.0001 ENSG00000101972.14 STAG2 0.001047325 −0.187270211 0.0007 ENSG00000106290.10 TAF6 0.014175182 −0.210235711 0.00050041 ENSG00000140262.13 TCF12 0.025334533 −0.184064816     2E−10 ENSG00000105329.4 TGFB1 0.015301045 −0.221315351 0.0002 ENSG00000140332.11 TLE3 0.001343794 −0.227829431  1.9998E−08 ENSG00000164168.3 TMEM184C 0.015050183 −0.397412646 2.49998E−08 ENSG00000106609.11 TMEM248 0.005316307 −0.23621242 2.89971E−07 ENSG00000204178.5 TMEM57 0.010544799 −0.345157048 0.00030006 ENSG00000169905.7 TOR1AIP2 0.025144824 −0.223803399 0.00070005 ENSG00000088325.11 TPX2 0.000751758 −0.147886462     4E−13 ENSG00000154370.8 TRIM11 0.010190424 −0.431525912 0.00030064 ENSG00000136878.7 USP20 0.019165529 −0.206602358  1.9998E−08 ENSG00000062650.12 WAPAL 0.019004475 −0.211592796 0.00080001 ENSG00000109685.13 WHSC1 0.0222009 −0.153361985     1E−11 ENSG00000082898.12 XPO1 0.026533538 −0.106116515     1E−11 ENSG00000048405.5 ZNF800 0.020652909 −0.271097499 2.9997E−08

TABLE 6 Motifs and G-quadruplexes in rDiff positive Gene ID Gene Name rDiff (p-value) Translational Efficiency (p-value) log2(Translational Efficiency) Table 6A. rDiff genes with 12-mer motif ENSG00000088325 TPX2 4.00E−13 0.000751758 −0.147886462 ENSG00000055163 CYFIP2 6.00E−13 0.757974081 −0.02427969 ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000181222 POLR2A 1.00E−12 0.038830003 −0.102840994 ENSG00000136068 FLNB 2.90E−12 0.062111584 −0.409977879 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −0.012039575 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −0.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −0.092503983 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −0.152181062 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000086758 HUWE1 2.40E−11 0.464534104 −0.039863394 ENSG00000080345 RIF1 3.00E−11 0.722609171 0.022548991 ENSG00000078674 PCM1 5.00E−11 0.600752059 −0.058335335 ENSG00000131148 EMC8 5.00E−11 0.89007858 −0.019540666 ENSG00000198231 DDX42 6.00E−11 0.824728919 −0.015904689 ENSG00000165417 GTF2A1 7.00E−11 0.844760071 −0.015019218 ENSG00000104738 MCM4 1.00E−10 0.915393017 0.003107424 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000110713 NUP98 1.00E−10 0.656641011 −0.027832725 ENSG00000148773 MKI67 1.00E−10 0.123777629 0.063404366 ENSG00000055483 USP36 2.00E−10 0.857880476 0.014047197 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000197694 SPTAN1 2.00E−10 0.081327953 −0.18679623 ENSG00000087460 GNAS 3.00E−10 0.461136397 −0.032870857 ENSG00000104517 UBR5 3.00E−10 0.744729033 0.031234126 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −0.150308959 ENSG00000124789 NUP153 3.20E−10 0.677271772 −0.045251116 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −0.208903322 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −0.205302853 ENSG00000084093 REST 1.00E−09 0.221405653 −0.118069779 ENSG00000101596 SMCHD1 1.00E−09 0.434566245 −0.059009881 ENSG00000125755 SYMPK 1.00E−09 0.552114085 −0.054422769 ENSG00000138795 LEF1 1.00E−09 1.60E−06 −0.210659864 ENSG00000172292 CERS6 1.00E−09 0.029552171 −0.205124483 ENSG00000198730 CTR9 1.00E−09 0.11470634 −0.142355213 ENSG00000013810 TACC3 2.00E−09 0.886452126 −0.009226853 ENSG00000101224 CDC25B 2.00E−09 0.25893922 0.059946483 ENSG00000137076 TLN1 2.00E−09 0.114582751 −0.09941367 ENSG00000143442 POGZ 2.00E−09 0.037681202 −0.207363006 ENSG00000157540 DYRK1A 2.00E−09 0.276566574 −0.107710063 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000165494 PCF11 2.00E−09 0.168402482 −0.149826279 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000132646 PCNA 4.00E−09 0.449582299 0.020688405 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000197081 IGF2R 4.10E−09 0.531193218 0.066454289 ENSG00000134954 ETS1 5.70E−09 1.27E−05 −0.232324455 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000114126 TFDP2 7.00E−09 0.567162468 −0.026000796 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000054654 SYNE2 9.00E−09 0.143319349 −0.17547751 ENSG00000101191 DIDO1 9.00E−09 0.846657226 −0.024545447 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000099381 SETD1A 1.00E−08 0.334979113 0.098318494 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000125686 MED1 1.00E−08 0.18711587 −0.124662129 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000135905 DOCK10 1.00E−08 0.717332641 0.040604232 ENSG00000135932 CAB39 1.00E−08 0.019948395 −0.200243436 ENSG00000139218 SCAF11 1.00E−08 0.50709776 −0.04074801 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000167522 ANKRD11 1.00E−08 0.255387498 0.10026816 ENSG00000167670 CHAF1A 1.00E−08 0.388610811 −0.064999638 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000125651 GTF2F1 1.10E−08 0.031215966 −0.168644284 ENSG00000171298 GAA 1.10E−08 0.092998845 −0.248293341 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000110321 EIF4G2 2.00E−08 0.4789335 −0.030452093 ENSG00000128191 DGCR8 2.00E−08 0.071123809 −0.242947421 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000144580 RQCD1 2.00E−08 0.506022372 −0.045037202 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000113522 RAD50 4.00E−08 0.22034331 0.108849135 ENSG00000115806 GORASP2 4.00E−08 0.107877983 −0.140430182 ENSG00000104886 PLEKHJ1 6.00E−08 0.445334658 0.068851577 ENSG00000110367 DDX6 6.00E−08 0.469603134 −0.047598358 ENSG00000084733 RAB10 7.00E−08 0.078220422 −0.136343032 ENSG00000140829 DHX38 8.00E−08 0.404193545 −0.083781852 ENSG00000158985 CDC42SE2 8.00E−08 0.027991366 −0.145160094 ENSG00000070756 PABPC1 1.00E−07 0.067231582 −0.133311245 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000103495 MAZ 1.30E−07 0.642227894 0.032737594 ENSG00000080815 PSEN1 1.50E−07 0.468385762 −0.105188191 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000002822 MAD1L1 1.70E−07 0.758278428 −0.03032717 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000138668 HNRNPD 2.40E−07 0.003261874 −0.098862205 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000136104 RNASEH2B 4.20E−07 0.392137768 0.057232924 ENSG00000135679 MDM2 4.90E−07 0.948348125 0.012834459 ENSG00000179262 RAD23A 5.10E−07 0.674786887 0.038029829 ENSG00000071626 DAZAP1 5.20E−07 0.060128417 −0.110195121 ENSG00000197930 ERO1L 6.50E−07 0.973303548 −0.003430597 ENSG00000118816 CCNI 6.90E−07 0.001528498 −0.189161037 ENSG00000179409 GEMIN4 7.20E−07 0.143223537 −0.152149612 ENSG00000074603 DPP8 1.09E−06 0.371935225 −0.109929668 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000064419 TNPO3 1.00E−04 0.030219393 −0.182349237 ENSG00000068796 KIF2A 1.00E−04 0.056041279 0.123499472 ENSG00000077097 TOP2B 1.00E−04 0.84957972 0.01045839 ENSG00000100401 RANGAP1 1.00E−04 0.59275986 −0.053239149 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000107854 TNKS2 1.00E−04 0.358901659 0.113182695 ENSG00000110651 CD81 1.00E−04 0.010480682 −0.130640591 ENSG00000111642 CHD4 1.00E−04 0.289163376 0.048737019 ENSG00000124181 PLCG1 1.00E−04 0.95873485 −0.001417988 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000138496 PARP9 1.00E−04 0.385276066 0.103537296 ENSG00000139350 NEDD1 1.00E−04 0.725169134 0.037847451 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000141556 TBCD 1.00E−04 0.591494459 −0.026526545 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000151702 FLI1 1.00E−04 0.221034285 −0.138078723 ENSG00000156875 HIAT1 1.00E−04 0.380713082 −0.10910263 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000166747 AP1G1 1.00E−04 0.033859721 −0.180376252 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000205629 LCMT1 1.00E−04 0.552673909 −0.089560402 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000148334 PTGES2 1.04E−04 0.626929001 −0.068481398 ENSG00000055130 CUL1 2.00E−04 0.24134893 −0.116033963 ENSG00000077232 DNAJC10 2.00E−04 0.043053807 −0.322931196 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000103222 ABCC1 2.00E−04 0.969797812 0.002188323 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000110619 CARS 2.00E−04 0.186855283 0.157414334 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000140525 FANCI 2.00E−04 0.688024573 0.029180218 ENSG00000144554 FANCD2 2.00E−04 0.730926111 0.036291397 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000151502 VPS26B 2.00E−04 0.277634848 0.100319458 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000177731 FLII 2.00E−04 0.139734019 0.11682969 ENSG00000196396 PTPN1 2.00E−04 0.634603291 0.040420571 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000072778 ACADVL 2.01E−04 0.634381953 0.052306846 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000185344 ATP6V0A2 2.03E−04 0.449082903 0.078626222 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000011295 TTC19 3.00E−04 0.726452954 0.048391976 ENSG00000036257 CUL3 3.00E−04 0.568119382 0.048886832 ENSG00000064115 TM7SF3 3.00E−04 0.921247137 0.007233323 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000167470 MIDN 3.00E−04 0.037975203 −0.404562969 ENSG00000167491 GATAD2A 3.00E−04 0.460886475 −0.052425426 ENSG00000169018 FEM1B 3.00E−04 0.01910054 −0.397020738 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000174238 PITPNA 3.00E−04 0.470422902 −0.066848619 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMG5 3.00E−04 0.489633279 0.073022366 ENSG00000205268 PDE7A 3.00E−04 0.558620633 −0.048541326 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000120738 EGR1 3.01E−04 0.317981925 −0.167567968 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000130402 ACTN4 3.01E−04 0.05655675 −0.168897398 ENSG00000073060 SCARB1 4.00E−04 0.444106259 −0.124760329 ENSG00000100242 SUN2 4.00E−04 0.443353969 0.107423956 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000119638 NEK9 4.00E−04 0.69912267 −0.04034303 ENSG00000140943 MBTPS1 4.00E−04 0.905572549 0.017038735 ENSG00000156983 BRPF1 4.00E−04 0.933570558 −0.010817335 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000072364 AFF4 4.01E−04 0.18444246 −0.147821651 ENSG00000198646 NCOA6 4.01E−04 0.116549501 −0.173636683 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000112200 ZNF451 5.00E−04 0.487557618 0.072986258 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000130816 DNMT1 5.00E−04 0.595705453 −0.027738247 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000100422 CERK 5.01E−04 0.767879843 −0.038668 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000033170 FUT8 6.00E−04 0.006226232 −0.355628717 ENSG00000063245 EPN1 6.00E−04 0.095672127 −0.260058118 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000115526 CHST10 6.00E−04 0.038600005 −0.351592853 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000184661 CDCA2 6.00E−04 0.129977922 −0.116602274 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000115020 PIKFYVE 7.00E−04 0.874274951 −0.045055571 ENSG00000120910 PPP3CC 7.00E−04 0.20233537 −0.200494687 ENSG00000133639 BTG1 7.00E−04 0.111632247 −0.307842825 ENSG00000143514 TP53BP2 7.00E−04 0.283581835 −0.117348193 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000169905 TOR1AIP2 7.00E−04 0.025144824 −0.223803399 ENSG00000102125 TAZ 7.01E−04 0.35021839 0.152681248 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000123983 ACSL3 7.01E−04 0.236015207 0.104976406 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000083312 TNPO1 8.00E−04 0.96323084 0.002633087 ENSG00000104472 CHRAC1 8.00E−04 0.353904047 0.105337178 ENSG00000105676 ARMC6 8.00E−04 0.830466125 −0.018392253 ENSG00000136824 SMC2 8.00E−04 0.373245909 0.054833376 ENSG00000168476 REEP4 8.00E−04 0.228797357 −0.127937767 ENSG00000173674 EIF1AX 8.00E−04 0.780846703 0.072635112 ENSG00000104852 SNRNP70 9.00E−04 0.594216034 −0.038334929 ENSG00000105486 LIG1 9.00E−04 0.865181674 −0.011170383 ENSG00000135521 LTV1 9.00E−04 0.577086029 0.047229663 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 ENSG00000185236 RAB11B 9.00E−04 0.250648111 −0.08681802 ENSG00000133961 NUMB 9.01E−04 0.646567716 0.059486807 Table 6B. rDiff genes with 9-mer motif ENSG00000088325 TPX2 4.00E−13 0.000751758 −0.147886462 ENSG00000055163 CYFIP2 6.00E−13 0.757974081 −0.02427969 ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000181222 POLR2A 1.00E−12 0.038830003 −0.102840994 ENSG00000136068 FLNB 2.90E−12 0.062111584 −0.409977879 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −0.012039575 ENSG00000055044 NOP58 1.00E−11 0.905915474 −0.006508419 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −0.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −0.092503983 ENSG00000108424 KPNB1 2.00E−11 8.66E−05 −0.171777065 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −0.152181062 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000086758 HUWE1 2.40E−11 0.464534104 −0.039863394 ENSG00000080345 RIF1 3.00E−11 0.722609171 0.022548991 ENSG00000139687 RB1 4.00E−11 0.227456544 0.062123731 ENSG00000078674 PCM1 5.00E−11 0.600752059 −0.058335335 ENSG00000131148 EMC8 5.00E−11 0.89007858 −0.019540666 ENSG00000162607 USP1 5.00E−11 0.111472525 −0.094654587 ENSG00000198231 DDX42 6.00E−11 0.824728919 −0.015904689 ENSG00000165417 GTF2A1 7.00E−11 0.844760071 −0.015019218 ENSG00000087087 SRRT 1.00E−10 0.966692349 0.001824104 ENSG00000104738 MCM4 1.00E−10 0.915393017 0.003107424 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000110713 NUP98 1.00E−10 0.656641011 −0.027832725 ENSG00000148773 MKI67 1.00E−10 0.123777629 0.063404366 ENSG00000174231 PRPF8 1.00E−10 0.595739886 0.019539188 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000140262 TCF12 2.00E−10 0.025334533 −0.184064816 ENSG00000197694 SPTAN1 2.00E−10 0.081327953 −0.18679623 ENSG00000087460 GNAS 3.00E−10 0.461136397 −0.032870857 ENSG00000104517 UBR5 3.00E−10 0.744729033 0.031234126 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −0.150308959 ENSG00000124789 NUP153 3.20E−10 0.677271772 −0.045251116 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −0.208903322 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −0.205302853 ENSG00000084093 REST 1.00E−09 0.221405653 −0.118069779 ENSG00000100554 ATP6V1D 1.00E−09 0.428461734 −0.082721884 ENSG00000101596 SMCHD1 1.00E−09 0.434566245 −0.059009881 ENSG00000125755 SYMPK 1.00E−09 0.552114085 −0.054422769 ENSG00000138795 LEF1 1.00E−09 1.60E−06 −0.210659864 ENSG00000172292 CERS6 1.00E−09 0.029552171 −0.205124483 ENSG00000198730 CTR9 1.00E−09 0.11470634 −0.142355213 ENSG00000013810 TACC3 2.00E−09 0.886452126 −0.009226853 ENSG00000066279 ASPM 2.00E−09 0.013635649 0.181712013 ENSG00000118193 KIF14 2.00E−09 0.302902759 0.10403347 ENSG00000137076 TLN1 2.00E−09 0.114582751 −0.09941367 ENSG00000143442 POGZ 2.00E−09 0.037681202 −0.207363006 ENSG00000151366 NDUFC2 2.00E−09 0.361312276 −0.043896664 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000165494 PCF11 2.00E−09 0.168402482 −0.149826279 ENSG00000204469 PRRC2A 2.00E−09 0.549464658 0.030387491 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000132646 PCNA 4.00E−09 0.449582299 0.020688405 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000197081 IGF2R 4.10E−09 0.531193218 0.066454289 ENSG00000134954 ETS1 5.70E−09 1.27E−05 −0.232324455 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000114126 TFDP2 7.00E−09 0.567162468 −0.026000796 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000054654 SYNE2 9.00E−09 0.143319349 −0.17547751 ENSG00000101191 DIDO1 9.00E−09 0.846657226 −0.024545447 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000099381 SETD1A 1.00E−08 0.334979113 0.098318494 ENSG00000099991 CABIN1 1.00E−08 0.104911155 −0.208959207 ENSG00000109332 UBE2D3 1.00E−08 0.601564183 0.04567695 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000125686 MED1 1.00E−08 0.18711587 −0.124662129 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000134313 KIDINS220 1.00E−08 0.857549373 0.021963698 ENSG00000135905 DOCK10 1.00E−08 0.717332641 0.040604232 ENSG00000135932 CAB39 1.00E−08 0.019948395 −0.200243436 ENSG00000139218 SCAF11 1.00E−08 0.50709776 −0.04074801 ENSG00000155827 RNF20 1.00E−08 0.674024322 0.06246891 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000167522 ANKRD11 1.00E−08 0.255387498 0.10026816 ENSG00000167670 CHAF1A 1.00E−08 0.388610811 −0.064999638 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000125651 GTF2F1 1.10E−08 0.031215966 −0.168644284 ENSG00000171298 GAA 1.10E−08 0.092998845 −0.248293341 ENSG00000175216 CKAP5 1.50E−08 0.03814885 0.117491174 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000084774 CAD 2.00E−08 0.242515439 0.087577807 ENSG00000110321 EIF4G2 2.00E−08 0.4789335 −0.030452093 ENSG00000128191 DGCR8 2.00E−08 0.071123809 −0.242947421 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000144580 RQCD1 2.00E−08 0.506022372 −0.045037202 ENSG00000171608 PIK3CD 2.00E−08 0.621359547 −0.054808961 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000164168 TMEM184C 2.50E−08 0.015050183 −0.397412646 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000108439 PNPO 3.00E−08 0.034630355 0.181670952 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000117906 RCN2 3.00E−08 0.060079639 0.177995705 ENSG00000130175 PRKCSH 3.00E−08 0.492538567 −0.034477239 ENSG00000136997 MYC 3.00E−08 0.000130485 −0.222358961 ENSG00000113522 RAD50 4.00E−08 0.22034331 0.108849135 ENSG00000115806 GORASP2 4.00E−08 0.107877983 −0.140430182 ENSG00000105677 TMEM147 5.00E−08 0.824197085 −0.020622451 ENSG00000135316 SYNCRIP 5.00E−08 0.141605449 −0.082838833 ENSG00000104886 PLEKHJ1 6.00E−08 0.445334658 0.068851577 ENSG00000110367 DDX6 6.00E−08 0.469603134 −0.047598358 ENSG00000188229 TUBB4B 6.00E−0S 0.176644347 0.091849122 ENSG00000084733 RAB10 7.00E−08 0.078220422 −0.136343032 ENSG00000140829 DHX38 S.00E−08 0.404193545 −0.083781852 ENSG00000158985 CDC42SE2 8.00E−08 0.027991366 −0.145160094 ENSG00000166986 MARS 9.00E−08 0.040009981 −0.120193487 ENSG00000070756 PA8PC1 1.00E−07 0.067231582 −0.13331124S ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000103495 MAZ 1.30E−07 0.642227894 0.032737594 ENSG00000080815 PSEN1 1.50E−07 0.468385762 −0.105188191 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000002822 MAD1L1 1.70E−07 0.758278428 −0.03032717 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000120800 UTP20 1.80E−07 0.730921404 0.032446721 ENSG00000167747 C19orf48 1.80E−07 0.222151707 −0.136113219 ENSG00000132155 RAF1 1.90E−07 0.727868161 0.035824977 ENSG00000138668 HNRNPD 2.40E−07 0.003261874 −0.098862205 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000196230 TUBB 2.40E−07 0.534866787 0.035871882 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000198276 UCKL1 3.30E−07 0.304042297 −0.145350623 ENSG00000136104 RNASEH2B 4.20E−07 0.392137768 0.057232924 ENSG00000135679 MDM2 4.90E−07 0.948348125 0.012834459 ENSG00000179262 RAD23A 5.10E−07 0.674786887 0.038029829 ENSG00000071626 DAZAP1 5.20E−07 0.060128417 −0.110195121 ENSG00000115053 NCL 5.50E−07 0.060545427 0.042909924 ENSG00000197930 ERO1L 6.50E−07 0.973303548 −0.003430597 ENSG00000118816 CCNI 6.90E−07 0.001528498 −0.189161037 ENSG00300179409 GEMIN4 7.20E−07 0.143223537 −0.152149612 ENSG00000151694 ADAM17 7.30E−07 0.446223538 −0.1096626 ENSG00000074603 DPP8 1.09E−06 0.371935225 −0.109929668 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000132612 VPS4A 3.05E−06 0.187740524 −0.117542241 ENSG00000186480 INSIG1 3.08E−06 0.573173068 −0.037858571 ENSG00000149273 RPS3 2.35E−05 0.448604972 −0.041417003 ENSG00000038219 BOD1L1 1.00E−04 0.003376816 0.278967432 ENSG00000051523 CYBA 1.00E−04 0.816434248 0.0204381 ENSG00000068796 KIF2A 1.00E−04 0.056041279 0.123499472 ENSG00000072310 SREBF1 1.00E−04 0.744899078 −0.026352209 ENSG00000077097 TOP2B 1.00E−04 0.84957972 0.01045839 ENSG00000100401 RANGAP1 1.00E−04 0.59275986 −0.053239149 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000107854 TNKS2 1.00E−04 0.358901659 0.113182695 ENSG00000110651 CD81 1.00E−04 0.010480682 −0.130640591 ENSG00000111642 CHD4 1.00E−04 0.289163376 0.048737019 ENSG00000119041 GTF3C3 1.00E−04 0.862861391 0.021723507 ENSG00000124181 PLCG1 1.00E−04 0.95873485 −0.001417988 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000136758 YME1L1 1.00E−04 0.090002669 −0.100978955 ENSG00000139350 NEDD1 1.00E−04 0.725169134 0.037847451 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000141556 TBCD 1.00E−04 0.591494459 −0.026526545 ENSG00000142002 DPP9 1.00E−04 0.734190324 −0.049637386 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000156875 HIAT1 1.00E−04 0.380713082 −0.10910263 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000172775 FAM192A 1.00E−04 0.366617379 −0.209977577 ENSG00000178252 WDR6 1.00E−04 0.9305271 0.005862339 ENSG00000184432 COPB2 1.00E−04 0.99225242 0.000643147 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000205629 LCMT1 1.00E−04 0.552673909 −0.089560402 ENSG00000221829 FANCG 1.00E−04 0.38011695 0.102243151 ENSG00000038210 PI4K2B 1.01E−04 0.689067203 0.060060784 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000106459 NRF1 1.01E−04 0.323046456 −0.119510858 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000148334 PTGES2 1.04E−04 0.626929001 −0.068481398 ENSG00000055130 CUL1 2.00E−04 0.24134893 −0.116033963 ENSG00000077232 DNAJC10 2.00E−04 0.043053807 −0.322931196 ENSG00000088247 KHSRP 2.00E−04 0.673716802 −0.021332247 ENSG00000089053 ANAPC5 2.00E−04 0.71210468 −0.020762022 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000103222 ABCC1 2.00E−04 0.969797812 0.002188323 ENSG00000105221 AKT2 2.00E−04 0.381664023 −0.141483695 ENSG00000105329 TGFB1 2.00E−04 0.015301045 −0.221315351 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000111906 HDDC2 2.00E−04 0.810276479 −0.022306759 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000144554 FANCD2 2.00E−04 0.730926111 0.036291397 ENSG00000145833 DDX46 2.00E−04 0.23392151 0.072701228 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000151502 VPS26B 2.00E−04 0.277634848 0.100319458 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000144431 FLII 2.00E−04 0.139734019 0.11682969 ENSG00000196396 PTPN1 2.00E−04 0.634603291 0.040420571 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000111726 CMAS 2.01E−04 0.649986681 0.073406219 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000119403 PHF19 2.01E−04 0.072821269 0.168059289 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000100994 PTGB 2.02E−04 0.741200463 0.05467102 ENSG00000105401 CDC37 2.02E−04 0.182664767 0.098508161 ENSG00000185344 ATP6V0A2 2.03E−04 0.449082903 0.078626222 ENSG00000118007 STAG1 2.04E−04 0.802913741 −0.02813744 ENSG00000196700 ZNF512B 2.09E−04 0.699101376 0.063580592 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000011295 TTC19 3.00E−04 0.726452954 0.048391976 ENSG00000036257 CUL3 3.00E−04 0.568119382 0.048886832 ENSG00000064115 TM7SF3 3.00E−04 0.921247137 0.007233323 ENSG00000064490 RFXANK 3.00E−04 0.015800837 −0.324746409 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000124193 SRSF6 3.00E−04 0.119574817 0.116472581 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000137106 GRHPR 3.00E−04 0.415762699 −0.09172823 ENSG00000138081 FBXO11 3.00E−04 0.421443356 −0.098168828 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000167470 MIDN 3.00E−04 0.037975203 −0.404562969 ENSG00000167491 GATAD2A 3.00E−04 0.460886475 −0.052425426 ENSG00000169018 FEM1B 3.00E−04 0.01910054 −0.397020738 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000174238 PITPNA 3.00E−04 0.470422902 −0.066848619 ENSG00000175931 UBE2O 3.00E−04 0.447757287 0.068133312 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMG5 3.00E−04 0.489633279 0.073022366 ENSG00000205268 PDE7A 3.00E−04 0.558620633 −0.048541326 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000120738 EGR1 3.01E−04 0.317981925 −0.167567968 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000130402 ACTN4 3.01E−04 0.05655675 −0.168897398 ENSG00000131467 PSME3 3.01E−04 0.03715923 −0.116973165 ENSG00000154370 TRIM11 3.01E−04 0.010190424 −0.431525912 ENSG00000073060 SCARB1 4.00E−04 0.44106259 −0.124760329 ENSG00000093009 CDC45 4.00E−04 0.918341518 0.007977992 ENSG00000100242 SUN2 4.00E−04 0.443353969 0.107423956 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000104365 IKBKB 4.00E−04 0.474002406 0.087889302 ENSG00000105939 ZC3HAV1 4.00E−04 0.868091195 0.01093142 ENSG00000114867 EIF4G1 4.00E−04 0.49755475 0.028286796 ENSG00000115419 GLS 4.00E−04 0.000197719 −0.269875671 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000119638 NEK9 4.00E−04 0.69912267 −0.04034303 ENSG00000140943 MBTPS1 4.00E−04 0.905572549 0.017038735 ENSG00000156983 BRPF1 4.00E−04 0.933570558 −0.010817335 ENSG00000172795 DCP2 4.00E−04 0.294839777 0.094471533 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000072364 AFF4 4.01E−04 0.18444246 −0.147821651 ENSG00000135763 URB2 4.01E−04 0.668047421 0.04463194 ENSG00000198646 NCOA6 4.01E−04 0.116549501 −0.173636683 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000216490 IFI30 4.13E−04 0.518872644 −0.117960608 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000112200 ZNF451 5.00E−04 0.487557618 0.072986258 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000130816 DNMT1 5.00E−04 0.595705453 −0.027738247 ENSG00000132842 AP3B1 5.00E−04 0.894277559 0.020029663 ENSG00000138698 RAP1GDS1 5.00E−04 0.715002624 −0.035260421 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000174579 MSL2 5.00E−04 0.027763257 −0.205275001 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000186575 NF2 5.00E−04 0.511808 0.06843328 ENSG00000100422 CERK 5.01E−04 0.767879843 −0.038668 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000033170 FUT8 6.00E−04 0.006226232 −0.355628717 ENSG00000060491 OGFR 6.00E−04 0.881572577 −0.018437371 ENSG00000063245 EPN1 6.00E−04 0.095672127 −0.260058118 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000090372 STRN4 6.00E−04 0.942223216 0.00735298 ENSG00000115526 CHST10 6.00E−04 0.038600005 −0.351592853 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000109062 SLC9A3R1 6.01E−04 0.122301958 −0.064055136 ENSG00000167775 CD320 6.01E−04 0.822695325 0.022736769 ENSG00000197312 DDI2 6.01E−04 0.856181146 −0.025215686 ENSG00000011376 LARS2 6.02E−04 0.269847002 −0.142543886 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000115020 PIKFYVE 7.00E−04 0.874274951 −0.045055571 ENSG00000116133 DHCR24 7.00E−04 0.242618057 −0.119340931 ENSG00000120910 PPP3CC 7.00E−04 0.20233537 −0.200494687 ENSG00000133639 BTG1 7.00E−04 0.111632247 −0.307842825 ENSG00000143514 TP53BP2 7.00E−04 0.283581835 −0.117348193 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000169905 TOR1AIP2 7.00E−04 0.025144824 −0.223803399 ENSG00000021762 OSBPL5 7.01E−04 0.905417327 −0.030769757 ENSG00000102125 TAZ 7.01E−04 0.35021839 0.152681248 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000123983 ACSL3 7.01E−04 0.236015207 0.104976406 ENSG00000123213 NLN 7.02E−04 0.499519365 0.090955024 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000082212 ME2 8.00E−04 0.795777072 −0.028699073 ENSG00000083312 TNPO1 8.00E−04 0.96323084 0.002633087 ENSG00000104472 CHRAC1 8.00E−04 0.353904047 0.105337178 ENSG00000105676 ARMC6 8.00E−04 0.830466125 −0.018392253 ENSG00000138231 DBR1 8.00E−04 0.870540124 0.016538189 ENSG00000168476 REEP4 8.00E−04 0.228797357 −0.127937767 ENSG00000169221 TBC1D10B 8.00E−04 0.845261963 0.037666933 ENSG00000173674 EIF1AX 8.00E−04 0.780846703 0.072635112 ENSG00000177156 TALDO1 8.00E−04 0.975031972 −0.001808282 ENSG00000204713 TR1M27 8.00E−04 0.790207031 −0.026814299 ENSG00000139946 PELI2 8.01E−04 0.84869402 −0.030488571 ENSG00000174010 KLHL15 8.01E−04 0.770357983 −0.039693382 ENSG00000171861 RNMTL1 8.04E−04 0.07761122 0.249083661 ENSG00000171202 TMEM126A 8.07E−04 0.731670543 0.060950022 ENSG00000081791 KIAA0141 9.00E−04 0.905406058 −0.017374448 ENSG00000104852 SNRNP70 9.00E−04 0.594216034 −0.038334929 ENSG00000105486 LIG1 9.00E−04 0.865181674 −0.011170383 ENSG00000115761 NOL10 9.00E−04 0.442727268 0.090675848 ENSG00000136709 WDR33 9.00E−04 0.304508163 −0.081701638 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 ENSG00000184719 RNLS 9.00E−04 0.124096231 −0.160207128 ENSG00000185236 RAB11B 9.00E−04 0.250648111 −0.08681802 ENSG00000133961 NUMB 9.01E−04 0.646567716 0.059486807 Table 6C. rDiff genes with G-Quadruplex structure ENSG00000009954 BAZ1B 1.00E−12 0.813245824 .011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −.012039575 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −.092503983 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −.152181062 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000198231 DDX42 6.00E−11 0.824728919 −.015904689 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000104517 UBR5 3.00E−10 0.744729033 0.031234126 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −0.150308959 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −0.208903322 ENSG00000058668 ATP2B4 1.00E−09 0.000680955 −0.302809666 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −0.205302853 ENSG00000125755 SYMPK 1.00E−09 0.552114085 −0.054422769 ENSG00000172292 CERS6 1.00E−09 0.029552171 −0.205124483 ENSG00000013810 TACC3 2.00E−09 0.886452126 −0.009226853 ENSG00000066279 ASPM 2.00E−09 0.013635649 0.181712013 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000106628 POLD2 1.00E−08 0.658612976 −0.035385479 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000064613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000093094 OSGEP 2.00E−08 0.977762307 −0.002519015 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000171608 PIK3CD 2.00E−08 0.621359547 −0.054808961 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000116698 SMG7 6.00E−08 0.886915303 −0.013938554 ENSG00000102606 ARHGEF7 6.00E−08 0.279523802 −0.128921833 ENSG00000125885 MCM8 1.20E−07 0.740692289 −0.028115948 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000051523 CYBA 1.00E−04 0.816434248 0.0204381 ENSG00000086504 MRPL28 1.00E−04 0.056394 −0.151444666 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000122882 ECD 1.00E−04 0.79331662 0.025252457 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000143401 ANP32E 1.00E−04 0.915890957 0.004516508 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000163808 KIF15 1.00E−04 0.593535319 0.070077932 ENSG00000166888 STAT6 1.00E−04 0.047894287 −0.21884119 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000105329 TGFB1 2.00E−04 0.015301045 −0.221315351 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000129317 PUS7L 2.00E−04 0.653028133 −0.054700064 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.586689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000177731 FLII 2.00E−04 0.139734019 0.11682969 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000111726 CMAS 2.01E−04 0.649986681 0.073406219 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000064490 RFXANK 3.00E−04 0.015800837 −0.324746409 ENSG00000100029 PES1 3.00E−04 0.805834098 −0.019606907 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.064932902 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMG5 3.00E−04 0.489633279 0.073022366 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000114867 EIF4G1 4.00E−04 0.49755475 0.028286796 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GMB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000114416 FXR1 6.00E−04 0.827823905 0.018508158 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000184661 CDCA2 6.00E−04 0.129977922 −0.116602274 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000100911 PSME2 6.11E−04 0.954296798 −0.00949908 ENSG00000101972 STAG2 7.00E−04 0.001047325 −0.187270211 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000171202 TMEM126A 8.07E−04 0.731670543 0.060950022 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 Table 7A-C. Motifs and G-quadruplexes in rDiff positive genes.

TABLE 7A rDiff genes with 12-mer motif Gene ID Gene Name Diff (p-value) Translational Efficiency (p-value) log2(Translational Efficiency) ENSG00000088325 TPX2 4.00E−13 0.000751758 −0.147886462 ENSG00000055163 CYFIP2 6.00E−13 0.757974081 −0.02427969 ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000181222 POLR2A 1.00E−12 0.038830003 −0.102840994 ENSG00000136068 FLNB 2.90E−12 0.062111584 −0.409977879 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −0.012039575 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −0.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −0.092503983 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −0.152181062 ENSG00000163655 GM PS 2.00E−11 0.775716157 0.020676052 ENSG00000086758 HUWE1 2.40E−11 0.464534104 −0.039863394 ENSG00000080345 RIF1 3.00E−11 0.722609171 0.022548991 ENSG00000078674 PCM1 5.00E−11 0.600752059 −0.058335335 ENSG00000131148 EMC8 5.00E−11 0.89007858 −0.019540666 ENSG00000198231 DDX42 6.00E−11 0.824728919 −0.015904689 ENSG00000165417 GTF2A1 7.00E−11 0.844760071 −0.015019218 ENSG00000104738 MCM4 1.00E−10 0.915393017 0.003107424 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000109111 NUP98 1.00E−10 0.656641011 −0.027832725 ENSG00000148773 MK167 1.00E−10 0.123777629 0.063404366 ENSG00000055483 USP36 2.00E−10 0.857880476 0.014047197 ENSG00000114126 TFDP2 7.00E−09 0.567162468 −0.026000796 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000054654 SYNE2 9.00E−09 0.143319349 −0.17547751 ENSG00000101191 DIDO1 9.00E−09 0.846657226 −0.024545447 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000099381 SETD1A 1.00E−08 0.334979113 0.098318494 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000125686 MED1 1.00E−08 0.18711587 −0.124662129 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000135905 DOCK10 1.00E−08 0.717332641 0.040604232 ENSG00000135932 CAB39 1.00E−08 0.019948395 −0.200243436 ENSG00000139218 SCAF11 1.00E−08 0.50709776 −0.04074801 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000167522 ANKRD11 1.00E−08 0.255387498 0.10026816 ENSG00000167670 CHAF1A 1.00E−08 0.388610811 −0.064999638 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000125651 GTF2F1 1.10E−08 0.031215966 −0.168644284 ENSG00000171298 GAA 1.10E−08 0.092998845 −0.248293341 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000110321 EIF4G2 2.00E−08 0.4789335 −0.030452093 ENSG00000128191 DGCR8 2.00E−08 0.071123809 −0.242947421 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000144580 RQCD1 2.00E−08 0.506022372 −0.045037202 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000113522 RAD50 4.00E−08 0.22034331 0.108849135 ENSG00000115806 GORASP2 4.00E−08 0.107877983 −0.140430182 ENSG00000104886 PLEKHJ1 6.00E−08 0.445334658 0.068851577 ENSG00000110367 DDX6 6.00E−08 0.469603134 −0.047598358 ENSG00000084733 RAB10 7.00E−08 0.078220422 −0.136343032 ENSG00000140829 DHX38 8.00E−08 0.404193545 −0.083781852 ENSG00000158985 CDC42SE2 8.00E−08 0.027991366 −0.145160094 ENSG00000070756 PABPC1 1.00E−07 0.067231582 −0.133311245 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000103495 MAZ 1.30E−07 0.642227894 0.032737594 ENSG00000080815 PSEN1 1.50E−07 0.468385762 −0.105188191 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000002822 MAD1L1 1.70E−07 0.758278428 −0.03032717 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000138668 HNRNPD 2.40E−07 0.003261874 −0.098862205 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000136104 RNASEH2B 4.20E−07 0.392137768 0.057232924 ENSG00000135679 MDM2 4.90E−07 0.948348125 0.012834459 ENSG00000179262 RAD23A 5.10E−07 0.674786887 0.038029829 ENSG00000071626 DAZAP1 5.20E−07 0.060128417 −0.110195121 ENSG00000197930 ERO1L 6.50E−07 0.973303548 −0.003430597 ENSG00000118816 CCNI 6.90E−07 0.001528498 −0.189161037 ENSG00000179409 GEMIN4 7.20E−07 0.143223537 −0.152149612 ENSG00000074603 DPP8 1.09E−06 0.371935225 −0.109929668 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000064419 TNPO3 1.00E−04 0.030219393 −0.182349237 ENSG00000068796 KIF2A 1.00E−04 0.056041279 0.123499472 ENSG00000077097 TOP2B 1.00E−04 0.84957972 0.01045839 ENSG00000100401 RANGAP1 1.00E−04 0.59275986 −0.053239149 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000107854 TNKS2 1.00E−04 0.358901659 0.113182695 ENSG00000110651 CD81 1.00E−04 0.010480682 −0.130640591 ENSG00000111642 CHD4 1.00E−04 0.289163376 0.048737019 ENSG00000124181 PLCG1 1.00E−04 0.95873485 −0.001417988 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000138496 PARP9 1.00E−04 0.385276066 0.103537296 ENSG00000139350 NEDD1 1.00E−04 0.725169134 0.037847451 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000141556 TBCD 1.00E−04 0.591494459 −0.026526545 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000151702 FLI1 1.00E−04 0.221034285 −0.138078723 ENSG00000156875 HIAT1 1.00E−04 0.380713082 −0.10910263 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000166747 AP1G1 1.00E−04 0.033859721 −0.180376252 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000205629 LCMT1 1.00E−04 0.552673909 −0.089560402 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000148334 PTGES2 1.04E−04 0.626929001 −0.068481398 ENSG00000055130 CUL1 2.00E−04 0.24134893 −0.116033963 ENSG00000077232 DNAJC10 2.00E−04 0.043053807 −0.322931196 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000103222 ABCC1 2.00E−04 0.969797812 0.002188323 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000110619 CARS 2.00E−04 0.186855283 0.157414334 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000140525 FANCI 2.00E−04 0.688024573 0.029180218 ENSG00000144554 FANCD2 2.00E−04 0.730926111 0.036291397 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000151502 VPS26B 2.00E−04 0.277634848 0.100319458 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000177731 FLIT 2.00E−04 0.139734019 0.11682969 ENSG00000196396 PTPN1 2.00E−04 0.634603291 0.040420571 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000072778 ACADVL 2.01E−04 0.634381953 0.052306846 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000185344 ATP6V0A2 2.03E−04 0.449082903 0.078626222 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000011295 TTC19 3.00E−04 0.726452954 0.048391976 ENSG00000036257 CUL3 3.00E−04 0.568119382 0.048886832 ENSG00000064115 TM7SF3 3.00E−04 0.921247137 0.007233323 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000167470 MIDN 3.00E−04 0.037975203 −0.404562969 ENSG00000167491 GATAD2A 3.00E−04 0.460886475 −0.052425426 ENSG00000169018 FEM1B 3.00E−04 0.01910054 −0.397020738 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000174238 PITPNA 3.00E−04 0.470422902 −0.066848619 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMGS 3.00E−04 0.489633279 0.073022366 ENSG00000205268 PDE7A 3.00E−04 0.558620633 −0.048541326 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000120738 EGR1 3.01E−04 0.317981925 −0.167567968 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000130402 ACTN4 3.01E−04 0.05655675 −0.168897398 ENSG00000073060 SCARB1 4.00E−04 0.444106259 −0.124760329 ENSG00000100242 SUN2 4.00E−04 0.443353969 0.107423956 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000119638 NEK9 4.00E−04 0.69912267 −0.04034303 ENSG00000140943 MBTPS1 4.00E−04 0.905572549 0.017038735 ENSG00000156983 BRPF1 4.00E−04 0.933570558 −0.010817335 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000072364 AFF4 4.01E−04 0.18444246 −0.147821651 ENSG00000198646 NCOA6 4.01E−04 0.116549501 −0.173636683 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000112200 ZNF451 5.00E−04 0.487557618 0.072986258 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000130816 DNMT1 5.00E−04 0.595705453 −0.027738247 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000100422 CERK 5.01E−04 0.767879843 −0.038668 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000033170 FUT8 6.00E−04 0.006226232 −0.355628717 ENSG00000063245 EPN1 6.00E−04 0.095672127 −0.260058118 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000115526 CHST10 6.00E−04 0.038600005 −0.351592853 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000184661 CDCA2 6.00E−04 0.129977922 −0.116602274 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000115020 PIKFYVE 7.00E−04 0.874274951 −0.045055571 ENSG00000120910 PPP3CC 7.00E−04 0.20233537 −0.200494687 ENSG00000133639 BTG1 7.00E−04 0.111632247 −0.307842825 ENSG00000143514 TP53BP2 7.00E−04 0.283581835 −0.117348193 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000169905 TOR1AIP2 7.00E−04 0.025144824 −0.223803399 ENSG00000102125 TAZ 7.01E−04 0.35021839 0.152681248 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000123983 ACSL3 7.01E−04 0.236015207 0.104976406 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000083312 TNPO1 8.00E−04 0.96323084 0.002633087 ENSG00000104472 CHRAC1 8.00E−04 0.353904047 0.105337178 ENSG00000105676 ARMC6 8.00E−04 0.830466125 −0.018392253 ENSG00000136824 SMC2 8.00E−04 0.373245909 0.054833376 ENSG00000168476 REEP4 8.00E−04 0.228797357 −0.127937767 ENSG00000173674 EIF1AX 8.00E−04 0.780846703 0.072635112 ENSG00000104852 SNRNP70 9.00E−04 0.594216034 −0.038334929 ENSG00000105486 LIG1 9.00E−04 0.865181674 −0.011170383 ENSG00000135521 LTV1 9.00E−04 0.577086029 0.047229663 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 ENSG00000185236 RAB11B 9.00E−04 0.250648111 −0.08681802

ENSG00000133961 NUMB 9.01E-04 0.646567716 0.059486807

TABLE 7B rDiff genes with 9-mer motif Gene ID Gene Name rDiff (p-value) Translational Efficiency (p-value) log2(Translational efficiency) ENSG00000088325 TPX2 4.00E−13 0.000751758 −.147886462 ENSG00000055163 CYFIP2 6.00E−13 0.757974081 −0.02427969 ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000181222 POLR2A 1.00E−12 0.038830003 −.102840994 ENSG00000136068 FLNB 2.90E−12 0.062111584 −.409977879 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −.012039575 ENSG00000055044 NOP58 1.00E−11 0.905915474 −.006508419 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −.092503983 ENSG00000108424 KPNB1 2.00E−11 8.66E−05 −.171777065 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −0.152181062 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000086758 HUWE1 2.40E−11 0.464534104 −0.039863394 ENSG00000080345 RIF1 3.00E−11 0.722609171 0.022548991 ENSG00000139687 RB1 4.00E−11 0.227456544 0.062123731 ENSG00000078674 PCM1 5.00E−11 0.600752059 −0.058335335 ENSG00000131148 EMC8 5.00E−11 0.89007858 −0.019540666 ENSG00000162607 USP1 5.00E−11 0.111472525 −0.094654587 ENSG00000198231 DDX42 6.00E−11 0.824728919 −0.015904689 ENSG00000165417 GTF2A1 7.00E−11 0.844760071 −0.015019218 ENSG00000087087 SRRT 1.00E−10 0.966692349 0.001824104 ENSG00000104738 MCM4 1.00E−10 0.915393017 0.003107424 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −0.157573098 ENSG00000110713 NUP98 1.00E−10 0.656641011 −0.027832725 ENSG00000148773 MK167 1.00E−10 0.123777629 0.063404366 ENSG00000174231 PRPF8 1.00E−10 0.595739886 0.019539188 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000140262 TCF12 2.00E−10 0.025334533 −0.184064816 ENSG00000197694 SPTAN1 2.00E−10 0.081327953 −0.18679623 ENSG00000087460 GNAS 3.00E−10 0.461136397 −0.032870857 ENSG00000104517 UBRS 3.00E−10 0.744729033 0.031234126 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −0.150308959 ENSG00000124789 NUP153 3.20E−10 0.677271772 −0.045251116 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −0.208903322 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −0.205302853 ENSG00000084093 REST 1.00E−09 0.221405653 −0.118069779 ENSG00000100554 ATP6V1D 1.00E−09 0.428461734 −0.082721884 ENSG00000101596 SMCHD1 1.00E−09 0.434566245 −0.059009881 ENSG00000125755 SYMPK 1.00E−09 0.552114085 −0.054422769 ENSG00000138795 LEF1 1.00E−09 1.60E−06 −0.210659864 ENSG00000172292 CERS6 1.00E−09 0.029552171 −0.205124483 ENSG00000198730 CTR9 1.00E−09 0.11470634 −0.142355213 ENSG00000013810 TACC3 2.00E−09 0.886452126 −0.009226853 ENSG00000066279 ASPM 2.00E−09 0.013635649 0.181712013 ENSG00000118193 KIF14 2.00E−09 0.302902759 0.10403347 ENSG00000137076 TLN1 2.00E−09 0.114582751 −0.09941367 ENSG00000143442 POGZ 2.00E−09 0.037681202 −0.207363006 ENSG00000151366 NDUFC2 2.00E−09 0.361312276 −0.043896664 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000165494 PCF11 2.00E−09 0.168402482 −0.149826279 ENSG00000204469 PRRC2A 2.00E−09 0.549464658 0.030387491 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000132646 PCNA 4.00E−09 0.449582299 0.020688405 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000197081 IGF2R 4.10E−09 0.531193218 0.066454289 ENSG00000134954 ETS1 5.70E−09 1.27E−05 −0.232324455 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000114126 TFDP2 7.00E−09 0.567162468 −0.026000796 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000054654 SYNE2 9.00E−09 0.143319349 −0.17547751 ENSG00000101191 DIDO1 9.00E−09 0.846657226 −0.024545447 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000099381 SETD1A 1.00E−08 0.334979113 0.098318494 ENSG00000099991 CABIN1 1.00E−08 0.104911155 −0.208959207 ENSG00000109332 UBE2D3 1.00E−08 0.601564183 0.04567695 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000125686 MED1 1.00E−08 0.18711587 −0.124662129 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000134313 KIDINS220 1.00E−08 0.857549373 0.021963698 ENSG00000135905 DOCK10 1.00E−08 0.717332641 0.040604232 ENSG00000135932 CAB39 1.00E−08 0.019948395 −0.200243436 ENSG00000139218 SCAF11 1.00E−08 0.50709776 −0.04074801 ENSG00000155827 RNF20 1.00E−08 0.674024322 0.06246891 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000167522 ANKRD11 1.00E−08 0.255387498 0.10026816 ENSG00000167670 CHAF1A 1.00E−08 0.388610811 −0.064999638 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000125651 GTF2F1 1.10E−08 0.031215966 −0.168644284 ENSG00000171298 GAA 1.10E−08 0.092998845 −0.248293341 ENSG00000175216 CKAP5 1.50E−08 0.03814885 0.117491174 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000084774 CAD 2.00E−08 0.242515439 0.087577807 ENSG00000110321 EIF4G2 2.00E−08 0.4789335 −0.030452093 ENSG00000128191 DGCR8 2.00E−08 0.071123809 −0.242947421 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000144580 RQCD1 2.00E−08 0.506022372 −0.045037202 ENSG00000171608 PIK3CD 2.00E−08 0.621359547 −0.054808961 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000164168 TMEM184C 2.50E−08 0.015050183 −0.397412646 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000108439 PNPO 3.00E−08 0.034630355 0.181670952 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000117906 RCN2 3.00E−08 0.060079639 0.177995705 ENSG00000130175 PRKCSH 3.00E−08 0.492538567 −0.034477239 ENSG00000136997 MYC 3.00E−08 0.000130485 −0.222358961 ENSG00000113522 RAD50 4.00E−08 0.22034331 0.108849135 ENSG00000115806 GORASP2 4.00E−08 0.107877983 −0.140430182 ENSG00000105677 TMEM147 5.00E−08 0.824197085 −0.020622451 ENSG00000135316 SYNCRIP 5.00E−08 0.141605449 −0.082838833 ENSG00000104886 PLEKHJ1 6.00E−08 0.445334658 0.068851577 ENSG00000110367 DDX6 6.00E−08 0.469603134 −0.047598358 ENSG00000188229 TUBB4B 6.00E−08 0.176644347 0.091849122 ENSG00000084733 RAB10 7.00E−08 0.078220422 −0.136343032 ENSG00000140829 DHX38 8.00E−08 0.404193545 −0.083781852 ENSG00000158985 CDC42SE2 8.00E−08 0.027991366 −0.145160094 ENSG00000166986 MARS 9.00E−08 0.040009981 −0.120193487 ENSG00000070756 PABPC1 1.00E−07 0.067231582 −0.133311245 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000103495 MAZ 1.30E−07 0.642227894 0.032737594 ENSG00000080815 PSEN1 1.50E−07 0.468385762 −0.105188191 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000002822 MAD1L1 1.70E−07 0.758278428 −0.03032717 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000120800 UTP20 1.80E−07 0.730921404 0.032446721 ENSG00000167747 C19orf48 1.80E−07 0.222151707 −0.136113219 ENSG00000132155 RAF1 1.90E−07 0.727868161 0.035824977 ENSG00000138668 HNRNPD 2.40E−07 0.003261874 −0.098862205 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000196230 TUBB 2.40E−07 0.534866787 0.035871882 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000198276 UCKL1 3.30E−07 0.304042297 −0.145350623 ENSG00000136104 RNASEH2B 4.20E−07 0.392137768 0.057232924 ENSG00000135679 MDM2 4.90E−07 0.948348125 0.012834459 ENSG00000179262 RAD23A 5.10E−07 0.674786887 0.038029829 ENSG00000071626 DAZAP1 5.20E−07 0.060128417 −0.110195121 ENSG00000115053 NCL 5.50E−07 0.060545427 0.042909924 ENSG00000197930 ERO1L 6.50E−07 0.973303548 −0.003430597 ENSG00000118816 CCNI 6.90E−07 0.001528498 −0.189161037 ENSG00000179409 GEMIN4 7.20E−07 0.143223537 −0.152149612 ENSG00000151694 ADAM17 7.30E−07 0.446223538 −0.1096626 ENSG00000074603 DPP8 1.09E−06 0.371935225 −0.109929668 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000132612 VPS4A 3.05E−06 0.187740524 −0.117542241 ENSG00000186480 INSIG1 3.08E−06 0.573173068 −0.037858571 ENSG00000149273 RPS3 2.35E−05 0.448604972 −0.041417003 ENSG00000038219 BOD1L1 1.00E−04 0.003376816 0.278967432 ENSG00000051523 CYBA 1.00E−04 0.816434248 0.0204381 ENSG00000068796 KIF2A 1.00E−04 0.056041279 0.123499472 ENSG00000072310 SREBF1 1.00E−04 0.744899078 −0.026352209 ENSG00000077097 TOP2B 1.00E−04 0.84957972 0.01045839 ENSG00000100401 RANGAP1 1.00E−04 0.59275986 −0.053239149 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000107854 TNKS2 1.00E−04 0.358901659 0.113182695 ENSG00000110651 CD81 1.00E−04 0.010480682 −0.130640591 ENSG00000111642 CHD4 1.00E−04 0.289163376 0.048737019 ENSG00000119041 GTF3C3 1.00E−04 0.862861391 0.021723507 ENSG00000124181 PLCG1 1.00E−04 0.95873485 −0.001417988 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000136758 YME1L1 1.00E−04 0.090002669 −0.100978955 ENSG00000139350 NEDD1 1.00E−04 0.725169134 0.037847451 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000141556 TBCD 1.00E−04 0.591494459 −0.026526545 ENSG00000142002 DPP9 1.00E−04 0.734190324 −0.049637386 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000156875 HIAT1 1.00E−04 0.380713082 −0.10910263 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000172775 FAM192A 1.00E−04 0.366617379 −0.209977577 ENSG00000178252 WDR6 1.00E−04 0.9305271 0.005862339 ENSG00000184432 COPB2 1.00E−04 0.99225242 0.000643147 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000205629 LCMT1 1.00E−04 0.552673909 −0.089560402 ENSG00000221829 FANCG 1.00E−04 0.38011695 0.102243151 ENSG00000038210 P14K2B 1.01E−04 0.689067203 0.060060784 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000106459 NRF1 1.01E−04 0.323046456 −0.119510858 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000148334 PTGES2 1.04E−04 0.626929001 −0.068481398 ENSG00000055130 CUL1 2.00E−04 0.24134893 −0.116033963 ENSG00000077232 DNAJC10 2.00E−04 0.043053807 −0.322931196 ENSG00000088247 KHSRP 2.00E−04 0.673716802 −0.021332247 ENSG00000089053 ANAPCS 2.00E−04 0.71210468 −0.020762022 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000103222 ABCC1 2.00E−04 0.969797812 0.002188323 ENSG00000105221 AKT2 2.00E−04 0.381664023 −0.141483695 ENSG00000105329 TGFB1 2.00E−04 0.015301045 −0.221315351 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000111906 HDDC2 2.00E−04 0.810276479 −0.022306759 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000144554 FANCD2 2.00E−04 0.730926111 0.036291397 ENSG00000145833 DDX46 2.00E−04 0.23392151 0.072701228 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000151502 VPS26B 2.00E−04 0.277634848 0.100319458 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000177731 FLI I 2.00E−04 0.139734019 0.11682969 ENSG00000196396 PTPN1 2.00E−04 0.634603291 0.040420571 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000111726 CMAS 2.01E−04 0.649986681 0.073406219 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000119403 PHF19 2.01E−04 0.072821269 0.168059289 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000100994 PYGB 2.02E−04 0.741200463 0.05467102 ENSG00000105401 CDC37 2.02E−04 0.182664767 0.098508161 ENSG00000185344 ATP6VOA2 2.03E−04 0.449082903 0.078626222 ENSG00000118007 STAG1 2.04E−04 0.802913841 −0.02813744 ENSG00000196700 ZNF512B 2.09E−04 0.699101376 0.063580592 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000011295 TTC19 3.00E−04 0.726452954 0.048391976 ENSG00000036257 CUL3 3.00E−04 0.568119382 0.048886832 ENSG00000064115 TM7SF3 3.00E−04 0.921247137 0.007233323 ENSG00000064490 RFXANK 3.00E−04 0.015800837 −0.324746409 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000124193 SRSF6 3.00E−04 0.119574817 0.116472581 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000137106 GRHPR 3.00E−04 0.415762699 −0.09172823 ENSG00000138081 FBXO11 3.00E−04 0.421443356 −0.098168828 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000167470 MIDN 3.00E−04 0.037975203 −0.404562969 ENSG00000167491 GATAD2A 3.00E−04 0.460886475 −0.052425426 ENSG00000169018 FEM1B 3.00E−04 0.01910054 −0.397020738 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000174238 PITPNA 3.00E−04 0.470422902 −0.066848619 ENSG00000175931 UBE2O 3.00E−04 0.447757287 0.068133312 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMGS 3.00E−04 0.489633279 0.073022366 ENSG00000205268 PDE7A 3.00E−04 0.558620633 −0.048541326 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000120738 EGR1 3.01E−04 0.317981925 −0.167567968 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000130402 ACTN4 3.01E−04 0.05655675 −0.168897398 ENSG00000131467 PSME3 3.01E−04 0.03715923 −0.116973165 ENSG00000154370 TRIM11 3.01E−04 0.010190424 −0.431525912 ENSG00000073060 SCARB1 4.00E−04 0.444106259 −0.124760329 ENSG00000093009 CDC45 4.00E−04 0.918341518 0.007977992 ENSG00000100242 SUN2 4.00E−04 0.443353969 0.107423956 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000104365 IKBKB 4.00E−04 0.474002406 0.087889302 ENSG00000105939 ZC3HAV1 4.00E−04 0.868091195 0.01093142 ENSG00000114867 EIF4G1 4.00E−04 0.49755475 0.028286796 ENSG00000115419 GLS 4.00E−04 0.000197719 −0.269875671 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000119638 NEK9 4.00E−04 0.69912267 −0.04034303 ENSG00000140943 MBTPS1 4.00E−04 0.905572549 0.017038735 ENSG00000156983 BRPF1 4.00E−04 0.933570558 −0.010817335 ENSG00000172795 DCP2 4.00E−04 0.294839777 0.094471533 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000072364 AFF4 4.01E−04 0.18444246 −0.147821651 ENSG00000135763 URB2 4.01E−04 0.668047421 0.04463194 ENSG00000198646 NCOA6 4.01E−04 0.116549501 −0.173636683 ENSG00000186716 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000216490 IFI30 4.13E−04 0.518872644 −0.117960608 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000112200 ZNF451 5.00E−04 0.487557618 0.072986258 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 ENSG00000130816 DNMT1 5.00E−04 0.595705453 −0.027738247 ENSG00000132842 AP3B1 5.00E−04 0.894277559 0.020029663 ENSG00000138698 RAP1GDS1 5.00E−04 0.715002624 −0.035260421 ENSG00000167323 STIM1 5.00E−04 0.977475163 0.002228555 ENSG00000174579 MSL2 5.00E−04 0.027763257 −0.205275001 ENSG00000185262 UBALD2 5.00E−04 0.504061449 0.054009121 ENSG00000186575 NF2 5.00E−04 0.511808 0.06843328 ENSG00000100422 CERK 5.01E−04 0.767879843 −0.038668 ENSG00000102908 NFAT5 5.01E−04 0.225277986 −0.178477519 ENSG00000005955 GGNBP2 6.00E−04 0.626526855 −0.042670122 ENSG00000033170 FUT8 6.00E−04 0.006226232 −0.355628717 ENSG00000060491 OGFR 6.00E−04 0.881572577 −0.018437371 ENSG00000063245 EPN1 6.00E−04 0.095672127 −0.260058118 ENSG00000067225 PKM 6.00E−04 0.089243304 0.079429696 ENSG00000090372 STRN4 6.00E−04 0.942223216 0.00735298 ENSG00000115526 CHST10 6.00E−04 0.038600005 −0.351592853 ENSG00000132466 ANKRD17 6.00E−04 0.746590296 0.023300227 ENSG00000197323 TRIM33 6.00E−04 0.267737397 −0.112414388 ENSG00000198728 LDB1 6.00E−04 0.333004346 −0.147406224 ENSG00000033800 PIAS1 6.01E−04 0.942720076 0.005741934 ENSG00000075975 MKRN2 6.01E−04 0.98382419 0.004421651 ENSG00000109062 SLC9A3R1 6.01E−04 0.122301958 −0.064055136 ENSG00000167775 CD320 6.01E−04 0.822695325 0.022736769 ENSG00000197312 DDI2 6.01E−04 0.856181146 −0.025215686 ENSG00000011376 LARS2 6.02E−04 0.269847002 −0.142543886 ENSG00000104695 PPP2CB 7.00E−04 0.032333256 −0.321922476 ENSG00000115020 PIKFYVE 7.00E−04 0.874274951 −0.045055571 ENSG00000116133 DHCR24 7.00E−04 0.242618057 −0.119340931 ENSG00000120910 PPP3CC 7.00E−04 0.20233537 −0.200494687 ENSG00000133639 BTG1 7.00E−04 0.111632247 −0.307842825 ENSG00000143514 TP53BP2 7.00E−04 0.283581835 −0.117348193 ENSG00000165209 STRBP 7.00E−04 0.030348179 −0.279083308 ENSG00000169905 TOR1AIP2 7.00E−04 0.025144824 −0.223803399 ENSG00000021762 OSBPLS 7.01E−04 0.905417327 −0.030769757 ENSG00000102125 TAZ 7.01E−04 0.35021839 0.152681248 ENSG00000111737 RAB35 7.01E−04 0.267070813 −0.097986528 ENSG00000123983 ACSL3 7.01E−04 0.236015207 0.104976406 ENSG00000123213 NLN 7.02E−04 0.499519365 0.090955024 ENSG00000060237 WNK1 8.00E−04 0.614924113 −0.029766546 ENSG00000082212 ME2 8.00E−04 0.795777072 −0.028699073 ENSG00000083312 TNPO1 8.00E−04 0.96323084 0.002633087 ENSG00000104472 CHRAC1 8.00E−04 0.353904047 0.105337178 ENSG00000105676 ARMC6 8.00E−04 0.830466125 −0.018392253 ENSG00000138231 DBR1 8.00E−04 0.870540124 0.016538189 ENSG00000168476 REEP4 8.00E−04 0.228797357 −0.127937767 ENSG00000169221 TBC1DOB 8.00E−04 0.845261963 0.037666933 ENSG00000173674 EIF1AX 8.00E−04 0.780846703 0.072635112 ENSG00000177156 TALDO1 8.00E−04 0.975031972 −0.001808282 ENSG00000204713 TRIM27 8.00E−04 0.790207031 −0.026814299 ENSG00000139946 PELI2 8.01E−04 0.84869402 −0.030488571 ENSG00000174010 KLHL15 8.01E−04 0.770357983 −0.039693382 ENSG00000171861 RNMTL1 8.04E−04 0.07761122 0.249083661 ENSG00000171202 TMEM126A 8.07E−04 0.731670543 0.060950022 ENSG00000081791 KIAA0141 9.00E−04 0.905406058 −0.017374448 ENSG00000104852 SNRNP70 9.00E−04 0.594216034 −0.038334929 ENSG00000105486 LIG1 9.00E−04 0.865181674 −0.011170383 ENSG00000115761 NOL10 9.00E−04 0.442727268 0.090675848 ENSG00000136709 WDR33 9.00E−04 0.304508163 −0.081701638 ENSG00000180104 EXOC3 9.00E−04 0.538380165 −0.070376673 ENSG00000184719 RNLS 9.00E−04 0.124096231 −0.160207128 ENSG00000185236 RAB11B 9.00E−04 0.250648111 −0.08681802 ENSG00000133961 NUMB 9.01E−04 0.646567716 0.059486807

TABLE 7C rDiff genes with G-Quadruplex structure Gene ID Gene Name rDiff (p-value) Translational Efficiency (p-value) log2(Translational Efficiency) ENSG00000009954 BAZ1B 1.00E−12 0.813245824 0.011597992 ENSG00000139613 SMARCC2 1.00E−12 0.334491125 0.087836839 ENSG00000127616 SMARCA4 3.00E−12 0.813848874 −.012039575 ENSG00000100796 SMEK1 1.00E−11 0.021404696 −.176469607 ENSG00000130726 TRIM28 1.00E−11 0.034098412 −.092503983 ENSG00000130724 CHMP2A 2.00E−11 0.770037849 0.028723436 ENSG00000152601 MBNL1 2.00E−11 0.00777836 −.152181062 ENSG00000163655 GMPS 2.00E−11 0.775716157 0.020676052 ENSG00000198231 DDX42 6.00E−11 0.824728919 −.015904689 ENSG00000105063 PPP6R1 1.00E−10 0.029786388 −.157573098 ENSG00000109111 SUPT6H 2.00E−10 0.994134615 0.001145357 ENSG00000104517 UBR5 3.00E−10 0.744729033 0.031234126 ENSG00000171681 ATF7IP 3.00E−10 0.209720012 −.150308959 ENSG00000137845 ADAM10 9.00E−10 0.012053048 −.208903322 ENSG00000058668 ATP2B4 1.00E−09 0.000680955 −.302809666 ENSG00000082641 NFE2L1 1.00E−09 0.267959196 −.205302853 ENSG00000125755 SYM PK 1.00E−09 0.552114085 −.054422769 ENSG00000172292 CERS6 1.00E−09 0.029552171 −.205124483 ENSG00000013810 TACC3 2.00E−09 0.886452126 −.009226853 ENSG00000066279 ASPM 2.00E−09 0.013635649 0.181712013 ENSG00000164190 NIPBL 2.00E−09 0.303068767 −0.09710725 ENSG00000117713 ARID1A 2.10E−09 0.944760522 0.009363654 ENSG00000153827 TRIP12 2.80E−09 0.04819259 −0.171340571 ENSG00000164134 NAA15 4.00E−09 0.476257503 −0.043457933 ENSG00000149480 MTA2 6.00E−09 2.64E−05 −0.22354576 ENSG00000120733 KDM3B 8.00E−09 0.056284307 −0.188410685 ENSG00000184009 ACTG1 9.00E−09 0.153012011 0.060571337 ENSG00000068024 HDAC4 1.00E−08 0.08742941 −0.17058278 ENSG00000106628 POLD2 1.00E−08 0.658612976 −0.035385479 ENSG00000118482 PHF3 1.00E−08 0.873633816 0.012763981 ENSG00000127152 BCL11B 1.00E−08 5.40E−10 −0.517770746 ENSG00000163466 ARPC2 1.00E−08 0.883580647 0.005900615 ENSG00000173020 ADRBK1 1.00E−08 0.708537254 −0.02554542 ENSG00000108021 FAM208B 1.70E−08 0.236407718 −0.130316925 ENSG00000065613 SLK 2.00E−08 0.412051605 −0.115711529 ENSG00000092094 OSGEP 2.00E−08 0.977762307 −0.002519015 ENSG00000136878 USP20 2.00E−08 0.019165529 −0.206602358 ENSG00000140332 TLE3 2.00E−08 0.001343794 −0.227829431 ENSG00000171608 PIK3CD 2.00E−08 0.621359547 −0.054808961 ENSG00000123066 MED13L 2.20E−08 4.79E−05 −0.415941737 ENSG00000048405 ZNF800 3.00E−08 0.020652909 −0.271097499 ENSG00000116698 SMG7 3.00E−08 0.886915303 −0.013938554 ENSG00000102606 ARHGEF7 6.00E−08 0.279523802 −0.128921833 ENSG00000125885 MCM8 1.20E−07 0.740692289 −0.028115948 ENSG00000171310 CHST11 1.20E−07 0.004536717 −0.14604981 ENSG00000184007 PTP4A2 1.50E−07 0.00039459 −0.142942918 ENSG00000071564 TCF3 1.70E−07 0.851040343 −0.020991025 ENSG00000171522 PTGER4 2.40E−07 0.002288634 −0.274827847 ENSG00000106609 TMEM248 2.90E−07 0.005316307 −0.23621242 ENSG00000079805 DNM2 1.53E−06 0.594275253 −0.034637408 ENSG00000051523 CYBA 1.00E−04 0.816434248 0.0204381 ENSG00000086504 MRPL28 1.00E−04 0.056394 −0.151444666 ENSG00000104613 INTS10 1.00E−04 0.796914737 0.022823898 ENSG00000122882 ECD 1.00E−04 0.79331662 0.025252457 ENSG00000136653 RASSF5 1.00E−04 0.545754108 −0.05276974 ENSG00000141027 NCOR1 1.00E−04 0.129071822 −0.136116164 ENSG00000143401 ANP32E 1.00E−04 0.915890957 0.004516508 ENSG00000143870 PDIA6 1.00E−04 0.042049362 0.102641235 ENSG00000157593 SLC35B2 1.00E−04 0.149940449 −0.2407324 ENSG00000160796 NBEAL2 1.00E−04 0.231202003 0.128523719 ENSG00000163808 KIF15 1.00E−04 0.593535319 0.070077932 ENSG00000166888 STAT6 1.00E−04 0.047894287 −0.21884119 ENSG00000167978 SRRM2 1.00E−04 0.027585188 −0.081656945 ENSG00000198911 SREBF2 1.00E−04 0.382129128 −0.081310955 ENSG00000204227 RING1 1.00E−04 0.123205251 −0.184910275 ENSG00000104825 NFKBIB 1.01E−04 0.438223723 0.114649527 ENSG00000125484 GTF3C4 1.01E−04 0.265749952 −0.128337377 ENSG00000089234 BRAP 2.00E−04 0.93786126 −0.010542696 ENSG00000105329 TGFB1 2.00E−04 0.015301045 −0.221315351 ENSG00000108175 ZMIZ1 2.00E−04 0.05690215 −0.222817452 ENSG00000129317 PUS7L 2.00E−04 0.653028133 −0.054700064 ENSG00000131504 DIAPH1 2.00E−04 0.005406879 −0.213577391 ENSG00000135090 TAOK3 2.00E−04 0.163787333 −0.139600964 ENSG00000147650 LRP12 2.00E−04 0.590549253 0.057987792 ENSG00000153310 FAM49B 2.00E−04 0.007506383 −0.139159484 ENSG00000160877 NACC1 2.00E−04 0.286689117 −0.119046325 ENSG00000163349 HIPK1 2.00E−04 0.020020123 −0.282659771 ENSG00000163904 SENP2 2.00E−04 0.045589218 −0.287466993 ENSG00000177731 FLII 2.00E−04 0.139734019 0.11682969 ENSG00000257103 LSM14A 2.00E−04 0.836442459 −0.017136198 ENSG00000111726 CMAS 2.01E−04 0.649986681 0.073406219 ENSG00000113580 NR3C1 2.01E−04 0.497681416 0.120970261 ENSG00000130311 DDA1 2.01E−04 0.855575658 −0.028673083 ENSG00000005007 UPF1 3.00E−04 0.109682217 −0.088407059 ENSG00000064490 RFXANK 3.00E−04 0.015800837 −0.324746409 ENSG00000100029 PES1 3.00E−04 0.805834098 −0.019606907 ENSG00000107164 FUBP3 3.00E−04 0.891753365 −0.016568849 ENSG00000112308 C6orf62 3.00E−04 0.221892591 −0.102283924 ENSG00000134371 CDC73 3.00E−04 0.078009542 −0.179882162 ENSG00000142453 CARM1 3.00E−04 0.397417148 −0.08333644 ENSG00000173442 EHBP1L1 3.00E−04 0.648913241 0.061932902 ENSG00000176619 LMNB2 3.00E−04 0.831805089 0.019798531 ENSG00000198952 SMG5 3.00E−04 0.489633279 0.073022366 ENSG00000214078 CPNE1 3.00E−04 0.910315945 −0.012942408 ENSG00000129355 CDKN2D 3.01E−04 0.933543847 −0.011782808 ENSG00000100697 DICER1 4.00E−04 0.937569952 0.007626111 ENSG00000114867 EIFG1 4.00E−04 0.49755475 0.028286796 ENSG00000115694 STK25 4.00E−04 0.063817944 −0.233874856 ENSG00000198087 CD2AP 4.00E−04 0.957505459 −0.006300497 ENSG00000167323 BCR 4.02E−04 0.28449305 −0.206113331 ENSG00000058063 ATP11B 5.00E−04 0.340893448 0.106997948 ENSG00000078369 GNB1 5.00E−04 0.011642786 −0.133797709 ENSG00000078618 NRD1 5.00E−04 0.441231318 −0.057082496 ENSG00000106290 TAF6 5.00E−04 0.014175182 −0.210235711 ENSG00000115548 KDM3A 5.00E−04 0.40321263 0.088419558 

What is claimed is:
 1. A method for identifying an agent capable of modulating cap-dependent mRNA translation, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein the modulation of translation in the presence of the agent indicates the agent as capable of modulating cap-dependent mRNA translation.
 2. The method of claim 1 wherein modulating is decreasing, suppressing or inhibiting cap-dependent mRNA translation.
 3. The method of claim 1 wherein the agent stabilizes the binding of eIF4A to the eIF4A-dependent translation-controlling motif of the mRNA.
 4. The method of claim 1 wherein the eIF4A-mRNA complex stabilizing motif of the mRNA is located in the 5′ UTR.
 5. The method of claim 1 wherein the eIF4A-dependent translation-controlling motif comprises a G-quadruplex structure.
 6. The method of claim 5 wherein the G-quadruplex structure comprises a (GGC/A)₄ motif.
 7. The method of claim 6 wherein the (GGC/A)₄ motif comprises GGCGGCGGCGGC (SEQ ID NO:1).
 8. The method of claim 1 wherein the eIF4A-dependent translation-controlling motif comprises a sequence selected from SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9 or SEQ ID NO:10.
 9. The method of claim 1 wherein the eIF4A-dependent translation-controlling motif comprises a sequence selected from SEQ ID NO:10 to SEQ ID NO:62.
 10. The method of claim 1 wherein the eIF4A-dependent translation-controlling motif is at least one sequence selected from SEQ ID NO:1 or from SEQ ID NO:4 to SEQ ID NO:62.
 15. The method of claim 1 wherein the mRNA encodes a transcription factor.
 16. The method of claim 1 wherein the mRNA encodes an oncogene.
 17. The method of claim 1 wherein the mRNA encodes NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 18. The method of claim 1 wherein the agent suppresses the growth of cancer cells in vitro or in vivo.
 19. The method of claim 1 wherein the agent interferes with eIF4A activity.
 20. The method of claim 1 wherein the agent increases eIF4A activity.
 21. The method of claim 1 wherein the agent inhibits eIF4A helicase activity.
 22. The method of claim 1 wherein the agent increases eIF4A helicase activity.
 23. The method of claim 1 wherein the agent promotes the stabilizing the binding of eIF4A with an eIF4A-dependent translation-controlling motif.
 24. The method of claim 1 wherein the agent does not trigger feedback activation of Akt.
 25. The method of any one of claims 1 to 24 wherein the modulation of translation is measured by a fluorescence reporter assay.
 26. The method of claim 25 wherein the assay comprises renilla luciferase expression.
 27. The method of claim 1 wherein the mRNA is from a gene selected from Table 3A.
 28. The method of claim 1 wherein the mRNA is from a gene selected from Table 3B.
 29. The method of claim 1 wherein the mRNA is from a gene selected from Table 3C.
 30. A method for identifying an agent that modulates eIF4A activity, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein the increase or decrease in translation efficiency in the presence of the agent indicates the agent as capable of increasing or decreasing eIF4A activity.
 31. A method for identifying an agent that inhibits eIF4A activity, the method comprising comparing translation efficiency in the presence and absence of the agent in an in-vitro or in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the agent as capable of inhibiting eIF4A activity.
 32. A method for determining whether an mRNA sequence comprises at least one eIF4A-dependent translation-controlling motif, the method comprising comparing translation efficiency in the presence and absence of an agent that inhibits eIF4A activity in an in-vivo translation system comprising eIF4A and an mRNA having one or more eIF4A-dependent translation-controlling motifs, wherein a decrease in translation efficiency in the presence of the agent indicates the mRNA sequence possesses at least one eIF4A-dependent translation-controlling motif.
 33. A method for determining whether a cancer or tumor is susceptible to an agent that inhibits eIF4A activity, the method comprising identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor, wherein the presence of the at least one eIF4A-dependent translation-controlling motif indicates susceptibility of the cancer or tumor to the agent.
 34. A method for determining whether a patient having cancer or a tumor will respond to treatment with an eIF4A inhibitor comprising the steps of 1) obtaining a sample of the cancer or tumor from the patient; and 2) identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor, wherein the presence of the at least one eIF4A-dependent translation-controlling motif indicates that the patient will respond to the treatment.
 35. The method of claim 33 or 34 wherein identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor is performed by comparing translation efficiency in the presence and absence of an eIF4A inhibitor agent in an in-vitro or in-vivo translation system comprising eIF4A and mRNA from the cancer or tumor, wherein a decrease in translation efficiency in the presence of the agent indicates the presence of an eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor.
 36. The method of claim 33 or 34 wherein identifying the presence of at least one eIF4A-dependent translation-controlling motif in mRNA from the cancer or tumor is performed by identifying a G-quadruplex motif in at least one oncogene in the cancer or tumor.
 37. The method of claim 36 wherein the motif is selected from among SEQ ID NO:1 and SEQ ID NO:4-62.
 38. A method for determining whether a patient having cancer or a tumor will respond to treatment with an eIF4A inhibitor comprising the steps of 1) obtaining a sample of the cancer or tumor from the patient; and 2) identifying the presence of at least one oncogene in the cancer or tumor described in Table 3A, 3B or 3C herein, wherein the presence of said at least one oncogene indicates that the patient will respond to the treatment.
 39. The method of any one of claims 33-38 where the presence of MYC does not indicate susceptibility or response to treatment.
 40. The method of any one of claims 33-39 wherein two or more methods are used to determine susceptibility or response to treatment.
 41. A method for preventing, treating or intervening in the recurrence of a cancer in a subject comprising administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer.
 42. The method of claim 41 wherein the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA.
 43. The method of claim 42 wherein the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif.
 44. The method of claim 43 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 45. The method of claim 43 wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 46. The method of claim 42 wherein the oncogenic mRNA comprises a G-quadruplex motif.
 47. The method of claim 42 wherein the oncogenic mRNA is from an oncogene.
 48. The method of claim 47 wherein the oncogene is selected from among Tables 3A, 3B and 3C.
 49. The method of claim 47 wherein the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 50. The method of claim 41 wherein the cancer is T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma, pancreatic cancer, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, non-small cell lung cancer, gastric cancer, Ewing sarcoma or lung adenocarcinoma.
 51. A method for preventing, treating or intervening in the recurrence of a cancer in a subject having an eIF4A dependent cancer, comprising administering to the subject an agent that blocks eIF4a helicase activity, thereby preventing, treating or intervening in the recurrence of the cancer.
 52. The method of claim 51 wherein the agent that blocks eIF4A helicase inhibits the translation of an oncogenic mRNA.
 53. The method of claim 53 wherein the oncogenic mRNA comprises an eIF4A-dependent translation-controlling motif.
 54. The method of claim 53 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 55. The method of claim 53 wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 56. The method of claim 52 wherein the oncogenic mRNA comprises a G-quadruplex motif.
 57. The method of claim 52 wherein the oncogenic mRNA is from an oncogene.
 58. The method of claim 57 wherein the oncogene is selected from among Tables 3A, 3B and 3C.
 59. The method of claim 57 wherein the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 60. The method of claim 51 wherein the cancer is T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma, pancreatic cancer, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, non-small cell lung cancer, gastric cancer, Ewing sarcoma or lung adenocarcinoma.
 61. A method for inhibiting in a subject the translation of an oncogene that comprises an eIF4A-dependent translation-controlling motif, the method comprising administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting translation of the oncogene.
 62. The method of claim 61 wherein translation of the oncogene causes cancer in the subject.
 63. The method of claim 61 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 64. The method of claim 5′ wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 65. The method of claim 61 wherein the mRNA of the oncogene comprises a G-quadruplex motif.
 66. The method of claim 61 wherein the oncogene is selected from among Tables 3A, 3B and 3C.
 67. The method of claim 61 wherein the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 68. The method of claim 62 wherein the cancer is T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma, pancreatic cancer, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, non-small cell lung cancer, gastric cancer, Ewing sarcoma or lung adenocarcinoma.
 69. A method for inhibiting in a subject eIF4A dependent mRNA translation, the method comprising administering to the subject an agent that blocks eIF4a helicase, thereby inhibiting mRNA translation.
 70. The method of claim 69 wherein the mRNA translation causes cancer in the subject.
 71. The method of claim 69 wherein the mRNA comprises an eIF4A-dependent translation-controlling motif.
 72. The method of claim 71 wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 73. The method of claim 71 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 74. The method of claim 69 wherein the mRNA encodes an oncogenic protein.
 75. The method of claim 74 wherein the oncogenic protein is encoded by an oncogene selected from among Tables 3A, 3B and 3C.
 76. The method of claim 74 wherein the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 77. The method of claim 70 wherein the cancer is T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma, pancreatic cancer, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, non-small cell lung cancer, gastric cancer, Ewing sarcoma or lung adenocarcinoma.
 78. A method for preventing in a subject the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif, the method comprising administering to the subject an agent that blocks eIF4a helicase activity, thereby inhibiting translation of the mRNA.
 79. The method of claim 78 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 80. The method of claim 78 wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 81. The method of claim 78 wherein the mRNA is from an oncogene selected from among Tables 3A, 3B and 3C.
 82. The method of claim 81 wherein the oncogene is NOTCH1, BCL11B, MYC, CDK6, RUNX1, BCL2 or MDM2.
 83. The method of claim 78 wherein the translation of the mRNA causes cancer.
 84. The method of claim 83 wherein the cancer is T-cell acute lymphoblastic leukemia, small cell lung cancer, renal cell carcinoma, squamous cell carcinoma of the head and neck, neuroblastoma, pancreatic cancer, transformed follicular lymphoma, mantel cell lymphoma, breast cancer, ovarian cancer, hepatocellular carcinoma, non-small cell lung cancer, gastric cancer, Ewing sarcoma or lung adenocarcinoma.
 85. The method of any one of claims 41-84 wherein the agent blocks the activity of eIF4A helicase.
 86. The method of any one of claims 41-84 wherein the agent blocks the translation of an mRNA comprising an eIF4A-dependent translation-controlling motif.
 87. The method of claim 86 wherein the eIF4A-dependent translation-controlling motif is a G-quadruplex motif.
 88. The method of any one of claims 41-87 wherein the eIF4A-dependent translation-controlling motif is selected from among SEQ ID NOs:1-62.
 89. The method of any one of claims 41-88 wherein the agent is a rocaglamide.
 90. The method of claim 89 wherein the rocaglamide is silvestrol, CR-31-B, or an analogue or derivative thereof.
 91. The method of any one of claims 34-88 wherein the agent is hippuristanol, pateamine A, or an analogue or derivative thereof.
 92. A method for measuring eIF4A helicase activity in vitro comprising contacting eIF4A helicase and ATP with a labeled oligonucleotide, said labeled oligonucleotide comprising a G-quadruplex sequence and a fluorophore at a 5′ or 3′ end and a fluorescence quencher at an other end, wherein interaction between the eIF4A helicase and the labeled oligonucleotide results in an increase in fluorescence of the labeled oligonucleotide correlated with eIF4A helicase activity.
 93. The method of claim 92 wherein the G-quadruplex sequence is selected from among SEQ ID NO:1-64.
 94. The method of claim 92 wherein the labeled oligonucleotide comprises SEQ ID NO:65.
 95. The method of claim 92 used for 1) measuring the effect of RNA helicases on G-quadruplex unwinding; 2) investigating the effect of cofactors/inhibitors required for eIF4A activity; 3) a screening method to identify other proteins that can unwind G-quadruplexes; and 4) identifying and establishing the effect of small molecules that stabilize the G-quadruplex structure.
 96. The method of claim 95 wherein the RNA helicase is eIF4A1, eIF4A2, DHX9 or DHX36.
 97. A labeled oligonucleotide comprising a G-quadruplex sequence selected from among SEQ ID NO:1-64 and a fluorophore at a 5′ or 3′ end and a fluorescence quencher at an other end.
 98. The labeled oligonucleotide of claim 97 comprising the sequence SEQ ID NO:65. 